Showing papers by "Stony Brook University published in 2002"

Oral language and code-related precursors to reading: Evidence from a longitudinal structural model.

Abstract: This study examined code-related and oral language precursors to reading in a longitudinal study of 626 children from preschool through 4th grade. Code-related precursors, including print concepts and phonological awareness, and oral language were assessed in preschool and kindergarten. Reading accuracy and reading comprehension skills were examined in 1st through 4th grades. Results demonstrated that (a) the relationship between code-related precursors and oral language is strong during preschool; (b) there is a high degree of continuity over time of both code-related and oral language abilities; (c) during early elementary school, reading ability is predominantly determined by the level of print knowledge and phonological awareness a child brings from kindergarten; and (d) in later elementary school, reading accuracy and reading comprehension appear to be 2 separate abilities that are influenced by different sets of skills.

Extensive mosaic structure revealed by the complete genome sequence of uropathogenic Escherichia coli

Abstract: We present the complete genome sequence of uropathogenic Escherichia coli, strain CFT073. A three-way genome comparison of the CFT073, enterohemorrhagic E. coli EDL933, and laboratory strain MG1655 reveals that, amazingly, only 39.2% of their combined (nonredundant) set of proteins actually are common to all three strains. The pathogen genomes are as different from each other as each pathogen is from the benign strain. The difference in disease potential between O157:H7 and CFT073 is reflected in the absence of genes for type III secretion system or phage- and plasmid-encoded toxins found in some classes of diarrheagenic E. coli. The CFT073 genome is particularly rich in genes that encode potential fimbrial adhesins, autotransporters, iron-sequestration systems, and phase-switch recombinases. Striking differences exist between the large pathogenicity islands of CFT073 and two other well-studied uropathogenic E. coli strains, J96 and 536. Comparisons indicate that extraintestinal pathogenic E. coli arose independently from multiple clonal lineages. The different E. coli pathotypes have maintained a remarkable synteny of common, vertically evolved genes, whereas many islands interrupting this common backbone have been acquired by different horizontal transfer events in each strain.

Positive Behavior Support: Evolution of an Applied Science

Abstract: Positive behavior support (PBS) is an applied science that uses educational and systems change methods (environmental redesign) to enhance quality of life and minimize problem behavior. PBS initial...

Goal-directed intraoperative fluid administration reduces length of hospital stay after major surgery.

Abstract: Background: Intraoperative hypovolemia is common and is a potential cause of organ dysfunction, increased postoperative morbidity, length of hospital stay, and death. The objective of this prospective, randomized study was to assess the effect of goal-directed intraoperative fluid administration on length of postoperative hospital stay. Methods: One hundred patients who were to undergo major elective surgery with an anticipated blood loss greater than 500 ml were randomly assigned to a control group (n 50) that received standard intraoperative care or to a protocol group (n 50) that, in addition, received intraoperative plasma volume expansion guided by the esophageal Doppler monitor to maintain maximal stroke volume. Length of postoperative hospital stay and postoperative surgical morbidity were assessed. Results: Groups were similar with respect to demographics, surgical procedures, and baseline hemodynamic variables. The protocol group had a significantly higher stroke volume and cardiac output at the end of surgery compared with the control group. Patients in the protocol group had a shorter duration of hospital stay compared with the control group: 5 3 versus 7 3 days (mean SD), with a median of 6 versus 7 days, respectively (P 0.03). These patients also tolerated oral intake of solid food earlier than the control group: 3 0.5 versus 4.7 0.5 days (mean SD), with a median of 3 versus 5 days, respectively (P 0.01). Conclusions: Goal-directed intraoperative fluid administration results in earlier return to bowel function, lower incidence of postoperative nausea and vomiting, and decrease in length of postoperative hospital stay. INTRAOPERATIVE hypovolemia is common and may be a potential cause of organ dysfunction, increased postoperative morbidity, and death. 1,2 Goal-directed plasma volume expansion during the intraoperative period is associated with improved outcome and reduction in hospital stay in patients undergoing cardiac and major orthopedic surgery. 3–5 The esophageal Doppler monitor (EDM) is an Food and Drug Administration–approved device that permits rapid, minimally invasive, and continuous estimation of cardiac output. 6 The cardiac output measurements obtained with the EDM have been shown to correlate well with the thermodilution method by different investigators. 7–11 Using the EDM to guide intraoperative plasma volume expansion, Sinclair et al. 4 demonstrated significant improvement in postoperative recovery and shortened hospital stay in patients undergoing proximal femoral neck fracture repair. Mythen and Webb, 3 in a study in cardiac patients, demonstrated a reduction in the incidence of gastrointestinal mucosal hypoperfusion and major complications in patients who received plasma volume optimization. In this study, we investigated whether goal-directed intraoperative plasma volume expansion guided by the EDM would shorten the length of hospital stay and improve postoperative outcomes (gastrointestinal and renal dysfunction) in patients undergoing moderate-risk surgery.

Chemical synthesis of poliovirus cDNA: generation of infectious virus in the absence of natural template.

Abstract: Full-length poliovirus complementary DNA (cDNA) was synthesized by assembling oligonucleotides of plus and minus strand polarity. The synthetic poliovirus cDNA was transcribed by RNA polymerase into viral RNA, which translated and replicated in a cell-free extract, resulting in the de novo synthesis of infectious poliovirus. Experiments in tissue culture using neutralizing antibodies and CD155 receptor-specific antibodies and neurovirulence tests in CD155 transgenic mice confirmed that the synthetic virus had biochemical and pathogenic characteristics of poliovirus. Our results show that it is possible to synthesize an infectious agent by in vitro chemical-biochemical means solely by following instructions from a written sequence.

Resilience to Loss and Chronic Grief: A Prospective Study From Preloss to 18-Months Postloss

Abstract: The vast majority of bereavement research is conducted after a loss has occurred. Thus, knowledge of the divergent trajectories of grieving or their antecedent predictors is lacking. This study gathered prospective data on 205 individuals several years prior to the death of their spouse and at 6- and 18-months postloss. Five core bereavement patterns were identified: common grief, chronic grief, chronic depression, improvement during bereavement, and resilience. Common grief was relatively infrequent, and the resilient pattern most frequent. The authors tested key hypotheses in the literature pertaining to chronic grief and resilience by identifying the preloss predictors of each pattern. Chronic grief was associated with preloss dependency and resilience with preloss acceptance of death and belief in a just world.

Transferring color to greyscale images

Abstract: We introduce a general technique for "colorizing" greyscale images by transferring color between a source, color image and a destination, greyscale image. Although the general problem of adding chromatic values to a greyscale image has no exact, objective solution, the current approach attempts to provide a method to help minimize the amount of human labor required for this task. Rather than choosing RGB colors from a palette to color individual components, we transfer the entire color "mood" of the source to the target image by matching luminance and texture information between the images. We choose to transfer only chromatic information and retain the original luminance values of the target image. Further, the procedure is enhanced by allowing the user to match areas of the two images with rectangular swatches. We show that this simple technique can be successfully applied to a variety of images and video, provided that texture and luminance are sufficiently distinct. The images generated demonstrate the potential and utility of our technique in a diverse set of application domains.

PIP2 and Proteins: Interactions, Organization, and Information Flow

Abstract: ▪ Abstract We review the physical properties of phosphatidylinositol 4,5-bisphosphate (PIP2) that determine both its specific interactions with protein domains of known structure and its nonspecific electrostatic sequestration by unstructured domains. Several investigators have postulated the existence of distinct pools of PIP2 within the cell to account for the myriad functions of this lipid. Recent experimental work indicates certain regions of the plasma membrane—membrane ruffles and nascent phagosomes—do indeed concentrate PIP2. We consider two mechanisms that could account for this phenomenon: local synthesis and electrostatic sequestration. We conclude by considering the hypothesis that proteins such as MARCKS bind a significant fraction of the PIP2 in a cell, helping to sequester it in lateral membrane domains, then release this lipid in response to local signals such as an increased concentration of Ca++/calmodulin or activation of protein kinase C.

Patient non-compliance with paper diaries

Abstract: Doctors often ask patients to recall recent health experiences, such as pain, fatigue, and quality of life1 Research has shown, however, that recall is unreliable and rife with inaccuracies and biases2 Recognition of recall's shortcomings has led to the use of diaries, which are intended to capture experiences close to the time of occurrence, thus limiting recall bias and producing more accurate data3 The rationale for using diaries would be undermined if patients failed to complete diaries according to protocol In this study we used a newly developed paper diary that could objectively record when patients made diary entries in order to compare patients' reported and actual compliance with diary keeping For comparison, we also used an electronic diary designed to enhance compliance in order to assess what compliance rates might be achieved We recruited 80 adults with chronic pain (pain for ≥3 hours a day and rated ≥4 on a 10 point scale) and assigned 40 to keeping a paper …

Capturing momentary, self-report data: a proposal for reporting guidelines.

Abstract: Self-report data are ubiquitous in behavioral and medical research. Retrospective assessment strategies are prone to recall bias and distortion. New techniques for assessing immediate experiences in respondents' natural environments (e.g., Ecological Momentary Assessment [1], Experience Sampling [2]) are being used by many researchers to reduce reporting bias. This article discusses seven aspects of momentary research that are often overlooked or minimized in the presentation of momentary research reports, yet that are critical to the success of the research: (a) the rationale for the momentary sampling design, (b) the details of momentary sampling procedures, (c) the data acquisition interface, (d) rates of compliance with the sampling plan, (e) the procedures used to train and monitor participants, (f) data management procedures, and (g) the data analytic approach. Attention to these areas in both the design and reporting of momentary research studies will not only improve momentary research protocols but also allow for the successful replication of research findings by other investigators.

Apparatus and method for fixation of vascular grafts

Abstract: An apparatus for facilitating securement of a vascular graft within a blood vessel, includes a shaft dimensioned for passage within a blood vessel and having an expansion member movable between a contracted condition and an expanded condition and a fastener array comprising at least one fastener disposed about a peripheral portion of the expansion member. The one fastener is deployable into a wall of the blood vessel upon movement of the expansion member to the expanded condition thereof, to thereby engage the vascular graft to secure the vascular graft to a wall of the blood vessel. The fastener array preferably includes a plurality of fasteners. The fasteners may be operatively connected to each other and releasably secured to the peripheral portion of the expansion member.

“Gender Symmetry” in Domestic Violence A Substantive and Methodological Research Review

Abstract: Despite numerous studies that report the preponderance of domestic violence is perpetrated by men against women, other empirical studies suggest that rates of domestic violence by women and men are equivalent. This article explores these claims of gender symmetry in intimate partners'use of violence by reviewing the empirical foundations of the research and critiquing existing sources of data on domestic violence. The author suggests methods to reconcile the disparate data and encourages researchers and practitioners to acknowledge women's use of violence while understanding why it tends to be very different from violence by men toward their female partners.

Randomized, comparative study of interferon beta-1a treatment regimens in MS: The EVIDENCE Trial.

Abstract: Background: Interferon β (IFNβ) reduces relapses and MRI activity in relapsing-remitting MS (RRMS), with variable effects on disability. The most effective dose regimen remains controversial. Methods: This randomized, controlled, multicenter trial compared the efficacy and safety of IFNβ-1a (Rebif®) 44 μg subcutaneously three times weekly (tiw), and IFNβ-1a (Avonex®) 30 μg IM once weekly (qw) in 677 patients with RRMS. Assessors blinded to treatment performed neurologic and MRI evaluations. The primary endpoint was the proportion of patients who were relapse free at 24 weeks; the principal MRI endpoint was the number of active lesions per patient per scan at 24 weeks. Results: After 24 weeks, 74.9% (254/339) of patients receiving IFNβ-1a 44 μg tiw remained relapse free compared with 63.3% (214/338) of those given 30 μg qw. The odds ratio for remaining relapse free was 1.9 (95% CI, 1.3 to 2.6; p = 0.0005) at 24 weeks and 1.5 (95% CI, 1.1 to 2.1; p = 0.009) at 48 weeks, favoring 44 μg tiw. Patients receiving 44 μg tiw had fewer active MRI lesions ( p p p = 0.002) and altered leukocyte counts (11% vs 5%, p = 0.003) compared with the 30 μg qw dosage. Neutralizing antibodies developed in 25% of 44 μg tiw patients and in 2% of patients receiving 30 μg qw. Conclusions: IFNβ-1a 44 μg subcutaneously tiw was more effective than IFNβ-1a 30 μg IM qw on all primary and secondary outcomes investigated after 24 and 48 weeks of treatment.

The Bax subfamily of Bcl2-related proteins is essential for apoptotic signal transduction by c-Jun NH(2)-terminal kinase.

Abstract: Targeted gene disruption studies have established that the c-Jun NH2-terminal kinase (JNK) signaling pathway is required for stress-induced release of mitochondrial cytochrome c and apoptosis. Here we demonstrate that activated JNK is sufficient to induce rapid cytochrome c release and apoptosis. However, activated JNK fails to cause death in cells deficient of members of the Bax subfamily of proapoptotic Bcl2-related proteins. Furthermore, exposure to stress fails to activate Bax, cause cytochrome c release, and induce death in JNK-deficient cells. These data demonstrate that proapoptotic members of the Bax protein subfamily are essential for JNK-dependent apoptosis.

Specification-based anomaly detection: a new approach for detecting network intrusions

Abstract: Unlike signature or misuse based intrusion detection techniques, anomaly detection is capable of detecting novel attacks. However, the use of anomaly detection in practice is hampered by a high rate of false alarms. Specification-based techniques have been shown to produce a low rate of false alarms, but are not as effective as anomaly detection in detecting novel attacks, especially when it comes to network probing and denial-of-service attacks. This paper presents a new approach that combines specification-based and anomaly-based intrusion detection, mitigating the weaknesses of the two approaches while magnifying their strengths. Our approach begins with state-machine specifications of network protocols, and augments these state machines with information about statistics that need to be maintained to detect anomalies. We present a specification language in which all of this information can be captured in a succinct manner. We demonstrate the effectiveness of the approach on the 1999 Lincoln Labs intrusion detection evaluation data, where we are able to detect all of the probing and denial-of-service attacks with a low rate of false alarms (less than 10 per day). Whereas feature selection was a crucial step that required a great deal of expertise and insight in the case of previous anomaly detection approaches, we show that the use of protocol specifications in our approach simplifies this problem. Moreover, the machine learning component of our approach is robust enough to operate without human supervision, and fast enough that no sampling techniques need to be employed. As further evidence of effectiveness, we present results of applying our approach to detect stealthy email viruses in an intranet environment.

Illustrations and guidelines for selecting statistical methods for quantifying spatial pattern in ecological data

Abstract: This paper aims to provide guidance to ecologists with limited experience in spatial analysis to help in their choice of techniques. It uses examples to compare methods of spatial analysis for ecological field data. A taxonomy of different data types is presented, including point- and area-referenced data, with and without attributes. Spatially and non-spatially explicit data are distinguished. The effects of sampling and other transformations that convert one data type to another are discussed; the possible loss of spatial information is considered. Techniques for analyzing spatial pattern, developed in plant ecology, animal ecology, landscape ecology, geostatistics and applied statistics are reviewed briefly and their overlap in methodology and philosophy noted. The techniques are categorized according to their output and the inferences that may be drawn from them, in a discursive style without formulae. Methods are compared for four case studies with field data covering a range of types. These are: 1) percentage cover of three shrubs along a line transect; 2) locations and volume of a desert plant in a 1 ha area; 3) a remotely-sensed spectral index and elevation from 105 km2 of a mountainous region; and 4) land cover from three rangeland types within 800 km2 of a coastal region. Initial approaches utilize mapping, frequency distributions and variance-mean indices. Analysis techniques we compare include: local quadrat variance, block quadrat variance, correlograms, variograms, angular correlation, directional variograms, wavelets, SADIE, nearest neighbour methods, Ripley's (t), and various landscape ecology metrics. Our advice to ecologists is to use simple visualization techniques for initial analysis, and subsequently to select methods that are appropriate for the data type and that answer their specific questions of interest. It is usually prudent to employ several different techniques.

Direct coupling of the cell cycle and cell death machinery by E2F.

Abstract: Unrestrained E2F activity forces S phase entry and promotes apoptosis through p53-dependent and -independent mechanisms. Here, we show that deregulation of E2F by adenovirus E1A, loss of Rb or enforced E2F-1 expression results in the accumulation of caspase proenzymes through a direct transcriptional mechanism. Increased caspase levels seem to potentiate cell death in the presence of p53-generated signals that trigger caspase activation. Our results demonstrate that mitogenic oncogenes engage a tumour suppressor network that functions at multiple levels to efficiently induce cell death. The data also underscore how cell cycle progression can be coupled to the apoptotic machinery.

Gene Co-Option in Physiological and Morphological Evolution

Abstract: Co-option occurs when natural selection finds new uses for existing traits, including genes, organs, and other body structures. Genes can be co-opted to generate developmental and physiological novelties by changing their patterns of regulation, by changing the functions of the proteins they encode, or both. This often involves gene duplication followed by specialization of the resulting paralogous genes into particular functions. A major role for gene co-option in the evolution of development has long been assumed, and many recent comparative developmental and genomic studies have lent support to this idea. Although there is relatively less known about the molecular basis of co-option events involving developmental pathways, much can be drawn from well-studied examples of the co-option of structural proteins. Here, we summarize several case studies of both structural gene and developmental genetic circuit co-option and discuss how co-option may underlie major episodes of adaptive change in multicellular organisms. We also examine the phenomenon of intraspecific variability in gene expression patterns, which we propose to be one form of material for the co-option process. We integrate this information with recent models of gene family evolution to provide a framework for understanding the origin of co-optive evolution and the mechanisms by which natural selection promotes evolutionary novelty by inventing new uses for the genetic toolkit.

Generation of spatially coherent light at extreme ultraviolet wavelengths.

Abstract: We present spatial coherence measurements of extreme ultraviolet (EUV) light generated through the process of high-harmonic up-conversion of a femtosecond laser. With a phase-matched hollow-fiber geometry, the generated beam was found to exhibit essentially full spatial coherence. The coherence of this laser-like EUV source was shown by recording Gabor holograms of small objects. This work demonstrates the capability to perform EUV holography with a tabletop experimental setup. Such an EUV source, with low divergence and high spatial coherence, can be used for experiments involving high-precision metrology, inspection of optical components for EUV lithography, and microscopy and holography with nanometer resolution. Furthermore, the short time duration of the EUV radiation (a few femtoseconds) will enable EUV microscopy and holography to be performed with ultrahigh time resolution.

A tone mapping algorithm for high contrast images

Abstract: A new method is presented that takes as an input a high dynamic range image and maps it into a limited range of luminance values reproducible by a display device. There is significant evidence that a similar operation is performed by early stages of human visual system (HVS). Our approach follows functionality of HVS without attempting to construct its sophisticated model. The operation is performed in three steps. First, we estimate local adaptation luminance at each point in the image. Then, a simple function is applied to these values to compress them into the required display range. Since important image details can be lost during this process, we then re-introduce details in the final pass over the image.

BORIS, a novel male germ-line-specific protein associated with epigenetic reprogramming events, shares the same 11-zinc-finger domain with CTCF, the insulator protein involved in reading imprinting marks in the soma

Abstract: CTCF, a conserved, ubiquitous, and highly versatile 11-zinc-finger factor involved in various aspects of gene regulation, forms methylation-sensitive insulators that regulate X chromosome inactivation and expression of imprinted genes We document here the existence of a paralogous gene with the same exons encoding the 11-zinc-finger domain as mammalian CTCF genes and thus the same DNA-binding potential, but with distinct amino and carboxy termini We named this gene BORIS for Brother of the Regulator of Imprinted Sites BORIS is present only in the testis, and expressed in a mutually exclusive manner with CTCF during male germ cell development We show here that erasure of methylation marks during male germ-line development is associated with dramatic up-regulation of BORIS and down-regulation of CTCF expression Because BORIS bears the same DNA-binding domain that CTCF employs for recognition of methylation marks in soma, BORIS is a candidate protein for the elusive epigenetic reprogramming factor acting in the male germ line

The effect of widowhood on older adults' social participation: an evaluation of activity, disengagement, and continuity theories.

Abstract: Purpose This study evaluated how levels of social participation change as a result of late-life widowhood. Social participation is a multidimensional construct incorporating both formal (e.g., meeting attendance, religious participation, and volunteer obligations) and informal (e.g., telephone contact and social interactions with friends) social roles. Design and methods Using data from the Changing Lives of Older Couples study, analyses compared widowed persons to continuously married control participants to evaluate whether widowhood affects older adults' levels of social participation. Results Widowed persons had higher levels of informal social participation than nonwidowed persons, whereas formal social participation levels were comparable between the two groups. Social participation levels decrease before the death of a spouse, primarily because of poor spousal health, and increase following the loss, because of increased support from friends and relatives. Implications Maintaining continuity in the realm of social participation is a strategy older adults use to cope with spousal loss; however, not all widowed persons have the same resources to alter their levels of social participation.

Synthesis and Characterization of Carbon Nanotube−Nanocrystal Heterostructures

Abstract: Oxidized single-walled carbon nanotubes (SWNTs) have been reacted with cadmium selenide (CdSe) nanocrystals, capped with mercaptothiol derivatives, as well as with titanium dioxide (TiO2) nanocrystals, functionalized with 11-aminoundecanoic acid to form nanoscale heterostructures, characterized by transmission electron microscopy and infrared spectroscopy. The reaction with acid-terminated CdSe nanocrystals and acid-terminated tubes was facilitated with the aid of intermediary linking agents, such as ethylenediamine and semicarbazide, in an amide-forming reaction in the presence of 1-ethyl-3-(3-dimethylaminopropyl) carbodiimide hydrochloride, EDC. Based on electronic absorption spectroscopy, charge transfer is thought to proceed from the nanocrystal to the nanotube in the CdSe−nanotube system, whereas in the TiO2−nanotube system, charge transfer is expected to occur from the nanotube to the nanocrystal.

ΔNp73, a dominant-negative inhibitor of wild-type p53 and TAp73, is up-regulated in human tumors

Abstract: p73 has significant homology to p53. However, tumor-associated up-regulation of p73 and genetic data from human tumors and p73-deficient mice exclude a classical Knudson-type tumor suppressor role. We report that the human TP73 gene generates an NH2 terminally truncated isoform. ΔNp73 derives from an alternative promoter in intron 3 and lacks the transactivation domain of full-length TAp73. ΔNp73 is frequently overexpressed in a variety of human cancers, but not in normal tissues. ΔNp73 acts as a potent transdominant inhibitor of wild-type p53 and transactivation-competent TAp73. ΔNp73 efficiently counteracts transactivation function, apoptosis, and growth suppression mediated by wild-type p53 and TAp73, and confers drug resistance to wild-type p53 harboring tumor cells. Conversely, down-regulation of endogenous ΔNp73 levels by antisense methods alleviates its suppressive action and enhances p53- and TAp73-mediated apoptosis. ΔNp73 is complexed with wild-type p53, as demonstrated by coimmunoprecipitation from cultured cells and primary tumors. Thus, ΔNp73 mediates a novel inactivation mechanism of p53 and TAp73 via a dominant-negative family network. Deregulated expression of ΔNp73 can bestow oncogenic activity upon the TP73 gene by functionally inactivating the suppressor action of p53 and TAp73. This trait might be selected for in human cancers.

A core-BRAF35 complex containing histone deacetylase mediates repression of neuronal-specific genes

Abstract: BRAF35, a structural DNA-binding protein, initially was identified as a component of a large BRCA2-containing complex. Biochemical analysis revealed the presence of a smaller core–BRAF35 complex devoid of BRCA2. Here we report the isolation of a six-subunit core–BRAF35 complex with the capacity to deacetylate histones, termed the BRAF–histone deacetylase complex (BHC), from human cells. BHC contains polypeptides reminiscent of the chromatin-remodeling complexes SWI/SNF and NuRD (nucleosome remodeling and deacetylating). Similar to NuRD, BHC contains an Mi2-like subunit, BHC80, and a PHD zinc-finger subunit as well as histone deacetylases 1/2 and an MTA-like subunit, the transcriptional corepressor CoREST. We show that BHC mediates repression of neuron-specific genes through the cis-regulatory element known as the repressor element 1 or neural restrictive silencer (RE1/NRS). Chromatin-immunoprecipitation experiments demonstrate the recruitment of BHC by the neuronal repressor REST. Expression of BRAF35 containing a single point mutation in the HMG domain of the protein abrogated REST-mediated transcriptional repression. These results demonstrate a role for core–BRAF35-containing complex in the regulation of neuron-specific genes through modulation of the chromatin structure.