Miracle-dz/UniFAR-FTUs huggingface dataset:
Hospitalization trends in adult ocular trauma at the University Hospital of the West Indies.

OBJECTIVE To assess the epidemiology of ocular trauma in adult patients admitted to the University Hospital of the West Indies (UHWI), Jamaica, between January 2000 and December 2005. METHODS Retrospective review of all adult patients admitted with ocular trauma in the UHWI trauma database. RESULTS Three hundred and ninety-seven patients were admitted with ocular trauma during the study period; 35.8% of admissions with ocular trauma were < or = 16 years of age. There were 252 adults (> 17 years old), 21.4% (54/252) were females and 78.6% (198/252) were males. The ratio of males to females was 3.7:1. The median age of the females and males was 32 years (95% CI 27, 35.9) and 33 years (95% CI 30, 35.0), respectively. The hospitalization period ranged from 1-283 days, mean 8.8 days in the males; and ranged from 1-39 days, mean six days in the females. March had the highest mean admissions over the six years. Severe chemical burns were the cause of the longest admissions. The most commonplace of injury was the home (30.2%) followed by in the street (28.2%); only 2% were from recreation. The most common cause of ocular injury was motor vehicle accident in 18.6%. The second most common cause was from nail hammering (14.3%); of this, 97.2% were male. Females (14.8%) were more commonly admitted from chemical injuries than males (11.1%). Of the females, 50% were due to domestic dispute and 50% were accidental bleach spills. CONCLUSION The most common cause of ocular injury was motor vehicle accidents, nail hammering in males and chemical injuries in females. Epidemiological information is important in determining the burden of ocular disease on the population. It is essential in planning improvement in health services and patient education for prevention of serious eye injuries.
Structured Stochastic Variational Inference

Stochastic variational inference makes it possible to approximate posterior distributions induced by large datasets quickly using stochastic optimization. The algorithm relies on the use of fully factorized variational distributions. However, this "mean-field" independence approximation limits the fidelity of the posterior approximation, and introduces local optima. We show how to relax the mean-field approximation to allow arbitrary dependencies between global parameters and local hidden variables, producing better parameter estimates by reducing bias, sensitivity to local optima, and sensitivity to hyperparameters.
Necl-4/SynCAM-4 Is Expressed in Myelinating Oligodendrocytes but Not Required for Axonal Myelination

The timing and progression of axonal myelination are precisely controlled by intercellular interactions between neurons and glia in development. Previous in vitro studies demonstrated that Nectin like 4 (Necl-4, also known as cell adhesion molecule Cadm-4 or SynCAM-4) plays an essential role in axonal myelination by Schwann cells in the peripheral nervous system (PNS). However, the role of Necl-4 protein in axonal myelination in the developing central nervous system (CNS) has remained unknown. In this study, we discovered upregulation of Necl-4 expression in mature oligodendrocytes at perinatal stages when axons undergo active myelination. We generated Necl4 gene knockout mice, but found that disruption of Necl-4 gene did not affect oligodendrocyte differentiation and myelin formation in the CNS. Surprisingly, disruption of Necl-4 had no significant effect on axonal myelination in the PNS either. Therefore, our results demonstrated that Necl-4 is dispensable for axonal myelination in the developing nervous system.
Protease inhibitors atazanavir, lopinavir and ritonavir are potent blockers, but poor substrates, of ABC transporters in a broad panel of ABC transporter-overexpressing cell lines.

OBJECTIVES A possible mechanism for HIV therapy failure is the efflux of HIV drugs from viral target cells or certain body compartments by ATP-binding cassette (ABC) transporters, allowing ongoing viral replication. Here, we investigated the interaction between protease inhibitors (PIs) and ABC transporters. METHODS To explore the potential blocking capacity of PIs, we exposed cells overexpressing multidrug resistance 1 P-glycoprotein (MDR1 P-gp), multidrug resistance protein 1 (MRP1) and breast cancer resistance protein (BCRP) to established cytotoxic substrates with or without one of the PIs atazanavir, lopinavir or ritonavir. Furthermore, to assess whether PIs serve as substrates, cell growth-inhibitory effects of these PIs were evaluated on cells overexpressing 1 of 11 ABC transporters and their parental counterparts. RESULTS Atazanavir, lopinavir and ritonavir were highly effective in reversing resistance against established substrates in cells overexpressing MDR1 P-gp and MRP1, and, to a lesser extent, BCRP. Concurrently, however, PIs appeared to be relatively poor substrates for ABC transporters. Only a moderate level of resistance to atazanavir was observed in cells overexpressing MRP6 and MRP9 [resistance factor (RF): 2.0-2.6]. Cells overexpressing MDR1 P-gp, MRP3, MRP4 and MRP5 displayed low levels of resistance to atazanavir (RF: 1.3-1.7); MRP7- and MRP9-overexpressing cells to lopinavir (RF: 1.4-1.5); and MRP9-overexpressing cells to ritonavir (RF: 1.4). CONCLUSIONS PIs can act as potent blockers of MDR1 P-gp, MRP1 and BCRP, but they are poor substrates for 11 ABC transporters. Consequently, ABC transporters are unlikely to play a major role in PI failure, but still may contribute to drug-specific adverse events and drug-drug interactions.
Atom: Horizontally Scaling Strong Anonymity

Atom is an anonymous messaging system that protects against traffic-analysis attacks. Unlike many prior systems, each Atom server touches only a small fraction of the total messages routed through the network. As a result, the system's capacity scales near-linearly with the number of servers. At the same time, each Atom user benefits from "best possible" anonymity: a user is anonymous among all honest users of the system, even against an active adversary who monitors the entire network, a portion of the system's servers, and any number of malicious users. The architectural ideas behind Atom have been known in theory, but putting them into practice requires new techniques for (1) avoiding heavy general-purpose multi-party computation protocols, (2) defeating active attacks by malicious servers at minimal performance cost, and (3) handling server failure and churn. Atom is most suitable for sending a large number of short messages, as in a microblogging application or a high-security communication bootstrapping ("dialing") for private messaging systems. We show that, on a heterogeneous network of 1,024 servers, Atom can transit a million Tweet-length messages in 28 minutes. This is over 23x faster than prior systems with similar privacy guarantees.
A description of children's verbal responses to a modern dance work in grades kindergarten through six

The purpose of this study was to describe the verbal responses that children make to a modern dance work on film before those children have received formal instruction in dance. A two-dimensional category system was designed for the purpose of classifying the subjects' verbal responses to the dance film. Valentine's (1962) classification scheme for children's verbal responses to paintings was the source for the four categories of dimension one. These categories were objective, expressive, associative, and subjective. Rudolf Laban's (1968) movement analysis framework was the source for the four categories of dimension two. These categories were body, effort, space, and relationship.
A Warm Heart and a Clear Head

Prior studies on the association between weather and psychological changes have produced mixed results. In part, this inconsistency may be because weather's psychological effects are moderated by two important factors: the season and time spent outside. In two correlational studies and an experiment manipulating participants' time outdoors (total N = 605), pleasant weather (higher temperature or barometric pressure) was related to higher mood, better memory, and “broadened” cognitive style during the spring as time spent outside increased. The same relationships between mood and weather were not observed during other times of year, and indeed hotter weather was associated with lower mood in the summer. These results are consistent with findings on seasonal affective disorder, and suggest that pleasant weather improves mood and broadens cognition in the spring because people have been deprived of such weather during the winter.
Parallel implementation of the steepest descent fast multipole method (SDFMM) on a Beowulf cluster for subsurface sensing applications

We present the parallel, MPI-based implementation of the SDFMM computer code using a thirty-two node Intel Pentium-based Beowulf cluster. The SDFMM is a fast algorithm that is a hybridization of the method of moments (MoMs), the fast multipole method (FMM), and the steepest descent integration path (SDP), which is used to solve large-scale linear systems of equations produced in electromagnetic scattering problems. An overall speedup of 7.2 has been achieved on the 32-processor Beowulf cluster and a significant reduced runtime is achieved on the 4-processor 667 MHz Alpha workstation.
Openness in adoption : Experiences and social psychological outcomes among birth mothers

SUMMARY This article describes the experiences of young, American birth mothers with regard to openness in adoption process and arrangement. Generally, larger proportions of the sample have experienced moderate, or semi-open, arrangements than those involving direct contact with the adoptive family. The associations between these experiences and a series of social psychological outcomes are examined at four years post-relinquishment. The data reveal that features of open adoption, e.g., visiting/phoning the adoptive family, have strong associations with long-term, positive outcomes for birth mothers. Perhaps equally important is the finding that several moderately open features which do not require direct or ongoing contact between birth mothers and adoptive families, e.g., birth mothers having a role in choosing the adoptive couple, are also strongly associated with positive outcomes. Policy implications are discussed.
Soft Tissue Sarcoma and Non‐Hodgkin's Lymphoma in Workers Exposed to Phenoxy Herbicides, Chlorophenols, and Dioxins: Two Nested Case‐Control Studies

We examined the effect of exposure to chemicals present in the production and spraying of phenoxy herbicides or chloro-phenols in two nested case-control studies of soft tissue sarcoma and non-Hodgkin's lymphoma. Eleven sarcoma and 32 lymphoma cases occurring within an international cohort were matched for age, sex, and country of residence with 55 and 158 controls, respectively. Exposures to 21 chemicals or mixtures were estimated by three industrial hygienists who were blind to the subject's case-control status. Excess risk of soft tissue sarcoma was associated with exposure to any phenoxy herbicide [odds ratio (OR) = 10.3; 95% confidence interval (Cl) = 1.2–91] and to each of the three major classes of phenoxy herbicides (2,4-dichlorophenoxyacetic acid, 2,4,5-trichloro-phenoxyacetic acid, and 4-chloro-2-methylphenoxyacetic acid), to any polychlorinated dibenzodioxin or furan (OR = 5.6; 95% CI = 1.1–28), and to 2,3,7,8-tetrachlorodibenzo-p-dioxm (OR = 5.2; 95% CI = 0.85–32). Sarcoma risk was not associated with exposure to raw materials or other process chemicals. In the non-Hodgkin's lymphoma study, associations were generally weaker than those found in the study on sarcoma. These findings indicate that workers exposed to phenoxy herbicides and their contaminants are at a higher risk of soft tissue sarcoma.
Deficiency for the Cysteine Protease Cathepsin L Impairs Myc-Induced Tumorigenesis in a Mouse Model of Pancreatic Neuroendocrine Cancer

Motivated by the recent implication of cysteine protease cathepsin L as a potential target for anti-cancer drug development, we used a conditional MycERTAM;Bcl-xL model of pancreatic neuroendocrine tumorigenesis (PNET) to assess the role of cathepsin L in Myc-induced tumor progression. By employing a cysteine cathepsin activity probe in vivo and in vitro, we first established that cathepsin activity increases during the initial stages of MycERTAM;Bcl-xL tumor development. Among the cathepsin family members investigated, only cathepsin L was predominately produced by beta-tumor cells in neoplastic pancreata and, consistent with this, cathepsin L mRNA expression was rapidly upregulated following Myc activation in the beta cell compartment. By contrast, cathepsins B, S and C were highly enriched in tumor-infiltrating leukocytes. Genetic deletion of cathepsin L had no discernible effect on the initiation of neoplastic growth or concordant angiogenesis. However, the tumors that developed in the cathepsin L-deficient background were markedly reduced in size relative to their typical wild-type counterparts, indicative of a role for cathepsin L in enabling expansive tumor growth. Thus, genetic blockade of cathepsin L activity is inferred to retard Myc-driven tumor growth, encouraging the potential utility of pharmacological inhibitors of cysteine cathepsins in treating late stage tumors.
BRAF Mutations in Advanced Cancers: Clinical Characteristics and Outcomes

Background Oncogenic BRAF mutations have been found in diverse malignancies and activate RAF/MEK/ERK signaling, a critical pathway of tumorigenesis. We examined the clinical characteristics and outcomes of patients with mutant (mut) BRAF advanced cancer referred to phase 1 clinic. Methods We reviewed the records of 80 consecutive patients with mutBRAF advanced malignancies and 149 with wild-type (wt) BRAF (matched by tumor type) referred to the Clinical Center for Targeted Therapy and analyzed their outcome. Results Of 80 patients with mutBRAF advanced cancer, 56 had melanoma, 10 colorectal, 11 papillary thyroid, 2 ovarian and 1 esophageal cancer. Mutations in codon 600 were found in 77 patients (62, V600E; 13, V600K; 1, V600R; 1, unreported). Multivariate analysis showed less soft tissue (Odds ratio (OR) = 0.39, 95%CI: 0.20–0.77, P = 0.007), lung (OR = 0.38, 95%CI: 0.19–0.73, p = 0.004) and retroperitoneal metastases (OR = 0.34, 95%CI: 0.13–0.86, p = 0.024) and more brain metastases (OR = 2.05, 95%CI: 1.02–4.11, P = 0.043) in patients with mutBRAF versus wtBRAF. Comparing to the corresponding wtBRAF, mutBRAF melanoma patients had insignificant trend to longer median survival from diagnosis (131 vs. 78 months, p = 0.14), while mutBRAF colorectal cancer patients had an insignificant trend to shorter median survival from diagnosis (48 vs. 53 months, p = 0.22). In melanoma, V600K mutations in comparison to other BRAF mutations were associated with more frequent brain (75% vs. 36.3%, p = 0.02) and lung metastases (91.6% vs. 47.7%, p = 0.007), and shorter time from diagnosis to metastasis and to death (19 vs. 53 months, p = 0.046 and 78 vs. 322 months, p = 0.024 respectively). Treatment with RAF/MEK targeting agents (Hazard ratio (HR) = 0.16, 95%CI: 0.03–0.89, p = 0.037) and any decrease in tumor size after referral (HR = 0.07, 95%CI: 0.015–0.35, p = 0.001) correlated with longer survival in mutBRAF patients. Conclusions BRAF appears to be a druggable mutation that also defines subgroups of patients with phenotypic overlap, albeit with differences that correlate with histology or site of mutation.
Distributed Private Data Analysis

We consider a distributed private data analysis setting, where multiple parties each hold some sensitive data and they wish to run a protocol to learn some aggregate statistics over the distributed dataset, while protecting each user’s privacy. As an initial effort, we consider a distributed summation problem. We first show a lower bound, that is, under information-theoretic differential privacy, any multi-party protocol with a small number of messages must have large additive error. We then show that by adopting a computational differential privacy notion, one can circumvent this lower bound and design practical protocols for the periodic distributed summation problem. Our construction has several desirable features. First, it works in the client-server model and requires no peer-to-peer communication among the clients. Second, our protocol is fault tolerant and can output meaningful statistics even when a subset of the participants fail to respond. Our constructions guarantee the privacy of honest parties even when a fraction of the participants may be compromised and colluding. In addition, we propose a new distributed noise addition mechanism that guarantees small total error.
Characterizing protein domain associations by Small-molecule ligand binding.

BACKGROUND Protein domains are evolutionarily conserved building blocks for protein structure and function, which are conventionally identified based on protein sequence or structure similarity. Small molecule binding domains are of great importance for the recognition of small molecules in biological systems and drug development. Many small molecules, including drugs, have been increasingly identified to bind to multiple targets, leading to promiscuous interactions with protein domains. Thus, a large scale characterization of the protein domains and their associations with respect to small-molecule binding is of particular interest to system biology research, drug target identification, as well as drug repurposing. METHODS We compiled a collection of 13,822 physical interactions of small molecules and protein domains derived from the Protein Data Bank (PDB) structures. Based on the chemical similarity of these small molecules, we characterized pairwise associations of the protein domains and further investigated their global associations from a network point of view. RESULTS We found that protein domains, despite lack of similarity in sequence and structure, were comprehensively associated through binding the same or similar small-molecule ligands. Moreover, we identified modules in the domain network that consisted of closely related protein domains by sharing similar biochemical mechanisms, being involved in relevant biological pathways, or being regulated by the same cognate cofactors. CONCLUSIONS A novel protein domain relationship was identified in the context of small-molecule binding, which is complementary to those identified by traditional sequence-based or structure-based approaches. The protein domain network constructed in the present study provides a novel perspective for chemogenomic study and network pharmacology, as well as target identification for drug repurposing.
Using Linear Mixed Models for Normalization of cDNA Microarrays

Microarrays are a tool for measuring the expression levels of a large number of genes simultaneously. In the microarray experiment, however, many undesirable systematic variations are observed. Correct identification and removal of these variations is essential to allow the comparison of expression levels across experiments. We describe the use of linear mixed models for the normalization of two-color spotted microarrays for various sources of variation including printtip variation. Normalization with linear mixed models provides a parametric model of which results compare favorably to intensity dependent normalization LOWESS methods. We illustrate the use of this technique on two datasets. The first dataset contains 24 arrays, each with approximately 600 genes, replicated 3 times per array. A second dataset, coming from the apo AI experiment, was used to further illustrate the methods. Finally, a simulation study was done to compare between methods.
Energy values of canola meal, cottonseed meal, bakery meal, and peanut flour meal for broiler chickens determined using the regression method

&NA; The energy values of canola meal (CM), cottonseed meal (CSM), bakery meal (BM), and peanut flour meal (PFM) for broiler chickens were determined in 2 experiments with Ross 708 broiler chickens from d 21 to 28 posthatch. The birds were fed a standard broiler starter diet from d 0 to 21 posthatch. In each experiment, 320 birds were grouped by weight into 8 blocks of 5 cages with 8 birds per cage and assigned to 5 diets. Each experiment used a corn‐soybean meal reference diet and 4 test diets in which test ingredients partly replaced the energy sources in the reference diet. The test diets in Exp. 1 consisted of 125 g CM, 250 g CM, 100 g CSM, or 200 g CSM/kg. In Exp. 2, the test diets consisted of 200 g BM, 400 g BM, 100 g PFM, or 200 g PFM/kg. The ileal digestible energy (IDE), metabolizable energy (ME), and nitrogen‐corrected metabolizable energy (MEn) of all the test ingredients were determined by the regression method. The DM of CM, CSM, BM and PFM were 883, 878, 878, and 964 g/kg, respectively and the respective gross energies (GE) were 4,143, 4,237, 4,060, and 5,783 kcal/kg DM. In Exp. 1, the IDE were 2,132 and 2,197 kcal/kg DM for CM and CSM, respectively. The ME were 2,286 and 2,568 kcal/kg DM for CM and CSM, respectively. The MEn were 1,931 kcal/kg DM for CM and 2,078 kcal/ kg DM for CSM. In Exp. 2, IDE values were 3,412 kcal/kg DM for BM and 4,801 kcal/kg DM for PFM; ME values were 3,176 and 4,601 kcal/kg DM for BM and PFM, respectively, and the MEn values were 3,093 kcal/kg DM for BM and 4,112 kcal/kg DM for PFM. In conclusion, the current study showed that chickens can utilize a considerable amount of energy from these 4 ingredients, and also provided the energy values of CM, CSM, BM and PFM for broiler chickens.
A Framework for Understanding the Critical Success Factors of Enterprise Business Intelligence Implementation

Implementation of a business intelligence (BI) system requires considerable resources. Although, the BI market appears vibrant and the importance of BI is widely accepted, few studies have investigated the Critical Success Factors (CSF) that affects its successful implementation. There is an imperative for a CSF approach to enable BI stakeholders to focus on the key issues that lead to successful BI systems implementation. This paper investigates the success factors and their contextual issues that may help organizations achieve a successful BI system implementation.
SNARE complex-mediated degranulation in mast cells

• Introduction • SNARE function in membrane fusion events • Expression of SNAREs and SNARE complexes in mast cells • Functional studies implicating specific SNAREs or SNARE complexes in mast cell degranulation • RNA interference studies, SNARES and mast cells • Regulation of mast cell SNAREs • Conclusions