Miracle-dz/UniFAR-FTUs huggingface dataset:
Demographic Pattern and Clinical Characteristics of Patients with Smear- Positive Pulmonary Tuberculosis in Kuwait

Objective: The aim of this study was to document various clinical factors that are likely to be of help in the control of tuberculosis in Kuwait. Subjects and Methods: Details of patients with sputum positive for acid-fast bacilli in the period from January 1998 to December 2000 were collected retrospectively from the case records and population statistics from government sources. The data were then tabulated and analyzed. Results: Of the 526 cases, 83.5% were expatriates and 16.5% Kuwaiti; 373 (70.9%) were male. Of the expatriates, 66.7% were from Asia and the Far East, 5.7% were ≧60 years. The annual incidence was 8.34 per 100,000 population. The lowest incidence was observed in the Jahrah governorate with an overall incidence of 5 (2.0 among Kuwaitis and 6.4 among expatriates) per 100,000 population. The highest incidence overall (10.2) and among Kuwaitis (4.1) was observed in the Farwaniya governorate, while the highest incidence among expatriates was seen in the Capital governorate (13.4). Radiologically, 94 (19.5%) had minimal, 246 (51.5%) had moderately advanced and 141 (29.3%) far-advanced disease. The majority of the patients (72%) had only + status for AFB in the smear. Hypercalcemia (25.7%), hyponatremia (22.15%) and hyperglycemia (29.9%) were common in the patients. Mean serum albumin was low (28.7 ± 5.5 g/l). Two hundred and forty-seven (47.2%) were declared cured while 116 (22.2%) completed treatment. Comparison between nationals and expatriates showed a significant difference only for age, smoking status, defaulter rate and place of residence. Conclusion: The lowest regional incidence was found in the Jahrah governorate. Both biochemical abnormalities and radiologically advanced presentations were common. Disease pattern and response to treatment was purely individual and did not differ with respect to nationality or race.
Quantitative Clinicopathologic Study of Senile Dementia

ABSTRACT: In a randomized blind study of 69 mental hospital patients over 50 years of age, a highly significant correlation was observed between the clinical symptoms of organic brain disease and the quantity of senile plaques found in the brains at autopsy. A stepwise multiple regression analysis indicated that independent significant predictors of the quantity of plaques were the level of disorientation and the age of the patient. Additional clinical tests for intellectual deterioration, affect lability, and impairment of memory and judgment did not improve the predictive ability. The correlation between incidental pathologic changes unrelated to the senile form of cerebral degeneration and the clinical symptoms was highly significant, though not obvious. Only after removal of the effect of the quantity of plaques on the clinical symptoms (multiple regression analysis) did the effect of other pathologic processes become evident. A significant one‐way fixed‐effect relationship was noted between increasing quantity of symptoms and increasing quantity of plaques in 48 cases of senile dementia correctly diagnosed by the psychiatry staff. In the control group of 21 patients without senile dementia, the quantity of plaques was correlated with the age of the patients but not with their clinical symptoms.
In Vivo Evolution of Tumor-Derived Endothelial Cells

The growth of a malignant tumor beyond a certain, limited size requires that it first develop an independent blood supply. In addition to providing metabolic support, this neovasculature also allows tumor cells to access the systemic circulation, thus facilitating metastatic dissemination. The neovasculature may originate either from normal blood vessels in close physical proximity to the tumor and/or from the recruitment of bone marrow-derived endothelial cell (EC) precursors. Recent studies have shown that human tumor vasculature ECs may also arise directly from tumor cells themselves and that the two populations have highly similar or identical karyotypes. We now show that, during the course of serial in vivo passage, these tumor-derived ECs (TDECs) progressively acquire more pronounced EC-like properties. These include higher-level expression of EC-specific genes and proteins, a greater capacity for EC-like behavior in vitro, and a markedly enhanced propensity to incorporate into the tumor vasculature. In addition, both vessel density and size are significantly increased in neoplasms derived from mixtures of tumor cells and serially passaged TDECs. A comparison of early- and late-passage TDECs using whole-genome single nucleotide polymorphism profiling showed the latter cells to have apparently evolved by a process of clonal expansion of a population with a distinct pattern of interstitial chromosomal gains and losses affecting a relatively small number of genes. The majority of these have established roles in vascular development, tumor suppression or epithelial-mesenchymal transition. These studies provide direct evidence that TDECs have a strong evolutionary capacity as a result of their inherent genomic instability. Consequently such cells might be capable of escaping anti-angiogenic cancer therapies by generating resistant populations.
Recent behavior of the Hadley cell and tropical thermodynamics in climate models and reanalyses

The behavior of the Hadley cell and the thermodynamic structure of the tropical atmosphere is analyzed over the period 1979–2000 in climate models and reanalyses. Significant trends in the strength of the Hadley cell are present in reanalyses that are not reproduced by models. Analysis of the thermodynamic structure also shows significant discrepancies between models and reanalyses, the former show warming aloft and increased static stability while the latter show a cooling trend and decreased static stability in the tropical mid‐troposphere. Additional energy balance analysis reveals that models and reanalyses have a fundamentally different balance between diabatic heating, circulation and thermodynamic structure over the period 1979–2000. Uncertainties in the observations of tropospheric temperatures as well as potential biases and errors in the climate models raise questions about the true long‐term behavior of the thermodynamic structure of the tropical troposphere and the Hadley cell.
An improved outer bound for multiterminal source coding

We prove a new outer bound on the rate-distortion region for the multiterminal source-coding problem. This bound subsumes the best outer bound in the literature and improves upon it strictly in some cases. The improved bound enables us to obtain a new, conclusive result for the binary erasure version of the "CEO problem. " The bound recovers many of the converse results that have been established for special cases of the problem, including the recent one for the Gaussian two-encoder problem.
Investigation of Bursting Forces in Post Tensioned Anchorage Zone

Three dimensional (3D) finite element (FE) analyses for post-tensioned anchorage zone were conducted to calculated bursting stress and bursting force. The structural behavior was investigated through the linear elastic finite element analyses with various design parameters such as the bearing plate size, the eccentricity, and the tendon inclination. Also effect of duct hole to bursting stress and bursting force was analysed with various diameter. Parametric analyses were followed to evaluate the relative contribution of all design parameters in determining the bursting force. Since the bursting force in AASHTO-LRFD is based on two dimensional anchorage model without duct hole, comparisons with the results and AASHTO-LRFD were conducted. Finally, an improved design guideline which considers the effect of the duct hole is suggested.
Treatment adherence with lithium and anticonvulsant medications among patients with bipolar disorder.

OBJECTIVE Nonadherence limits the effectiveness of medications among patients with bipolar disorder. This study examined adherence with lithium and anticonvulsant medication among patients with bipolar disorder receiving treatment in Department of Veterans Affairs (VA) settings. METHODS Patients receiving treatment in the VA for bipolar disorder during federal fiscal year 2003 (FY03) and receiving lithium or anticonvulsant medication were identified (N=44,637) by using the VA's National Psychosis Registry. Medication adherence was assessed by using the medication possession ratio (MPR) for lithium, valproate or divalproex, carbamazepine, and lamotrigine. Patients were categorized into three groups: fully adherent (MPR greater than .80), partially adherent (MPR from more than .50 to .80), and nonadherent (MPR less than or equal to .50). RESULTS A slight majority of individuals (54.1%) were fully adherent, 24.5% were partially adherent, and 21.4% were nonadherent. Nonadherent individuals were more likely to be younger, unmarried, nonwhite, or homeless or to have diagnoses of a substance use disorder or fewer outpatient psychiatric visits in FY03. Adherence intensity was somewhat lower for valproate, compared with lithium or other anticonvulsants. Individuals given prescriptions for two agents to stabilize mood had better adherence than individuals given prescriptions for a single agent. Unexpectedly, in multivariate analyses adjusting for prior hospitalization, number of outpatient psychiatric visits, and a diagnosis of substance use disorder, poorer adherence was associated with decreased rates of hospitalization. CONCLUSIONS Nearly one in two individuals given prescriptions for lithium or anticonvulsant medication to treat bipolar disorder did not take their medications as prescribed. The effectiveness of bipolar medication treatments is reduced by high rates of nonadherence in clinical settings.
Identification and Genomic Characterization of a New Virus (Tymoviridae Family) Associated with Citrus Sudden Death Disease

ABSTRACT Citrus sudden death (CSD) is a new disease that has killed approximately 1 million orange trees in Brazil. Here we report the identification of a new virus associated with the disease. RNAs isolated from CSD-affected and nonaffected trees were used to construct cDNA libraries. A set of viral sequences present exclusively in libraries of CSD-affected trees was used to obtain the complete genome sequence of the new virus. Phylogenetic analysis revealed that this virus is a new member of the genus Marafivirus. Antibodies raised against the putative viral coat proteins allowed detection of viral antigens of expected sizes in affected plants. Electron microscopy of purified virus confirmed the presence of typical isometric Marafivirus particles. The screening of 773 affected and nonaffected citrus trees for the presence of the virus showed a 99.7% correlation between disease symptoms and the presence of the virus. We also detected the virus in aphids feeding on affected trees. These results suggest that this virus is likely to be the causative agent of CSD. The virus was named Citrus sudden death-associated virus.
Differences in the DNA-binding properties of the HMG-box domains of HMG1 and the sex-determining factor SRY.

High-mobility-group protein 1 (HMG1) is an abundant, non-sequence-specific, chromosomal protein with two homologous, HMG-box, DNA-binding domains, A and B, and an acidic tail. The HMG-box motif also occurs, as a single copy, in some sequence-specific transcription factors, e.g. the sex-determining factor, SRY. We have investigated whether or not there are differences in the DNA-binding properties of the isolated A and B HMG-box domains of HMG1 and SRY and whether, in the case of A and B, there might also be differences due to different sequence contexts within the native protein. The basic regions that flank the HMG1 B box, giving B', enhance its DNA-binding, supercoiling and DNA-bending activities, and promote the self-association of the DNA-bound B-box. All the HMG-box domains bind with structure specificity to four-way junctions, but the structure selectivity is significantly greater for A and the SRY box than for the HMG1 B or B' domains, as judged by competition with excess plasmid DNA. The domains self-associate to different extents on supercoiled DNA and this may explain differences in the ability to discriminate between four-way junctions and supercoiled DNA. The HMG1 A, B and B' domains constrain negative superhelical turns in DNA, but the SRY HMG box does not. Only the full B domain (B') bends DNA in a ligase-mediated circularisation assay; the minimal B box, the A domain and the SRY box do not. Thus, despite a common global fold, the HMG box appears to have been adapted to various functions in different protein contexts.
EPIC: Ending Piracy of Integrated Circuits

As semiconductor manufacturing requires greater capital investments, the use of contract foundries has grown dramatically, increasing exposure to mask theft and unauthorized excess production. While only recently studied, IC piracy has now become a major challenge for the electronics and defense industries. We propose a novel comprehensive technique to end piracy of integrated circuits (EPIC). It requires that every chip be activated with an external key, which can only be generated by the holder of IP rights, and cannot be duplicated. EPIC is based on (i) automatically-generated chip IDs, (ii) a novel combinational locking algorithm, and (Hi) innovative use of public-key cryptography. Our evaluation suggests that the overhead of EPIC on circuit delay and power is negligible, and the standard flows for verification and test do not require change. In fact, major required components have already been integrated into several chips in production. We also use formal methods to evaluate combinational locking and computational attacks. A comprehensive protocol analysis concludes that EPIC is surprisingly resistant to various piracy attempts.
Characterization of Small-Colony Variants of Enterococcus faecalis Isolated from Chickens with Amyloid Arthropathy

ABSTRACT In this study we report the isolation and characterization of normal-sized and small-colony variants of Enterococcus faecalis from outbreaks of amyloid arthropathy in chickens. Postmortem examinations of 59 chickens revealed orange deposits in the knee joints, typical for amyloid arthropathy. Bacterial cultures from 102 joints and 43 spleens exhibited pure (n = 88) and mixed (n = 11) cultures of normal (n = 60) and pinpoint (n = 28) colonies of E. faecalis. Pulsed-field gel electrophoresis of 62 isolates demonstrated seven different band patterns with at most two band size variations, and multilocus sequence typing demonstrated two different sequence types, sharing six out of seven alleles, suggesting a close evolutionary relationship between isolates obtained from four outbreaks. In addition, all isolates were clonally related to an amyloid arthropathy reference strain from The Netherlands, previously shown to be globally dispersed. Initial investigation of the isolated small-colony variant phenotype revealed no difference in whole-cell protein profiling between normal and pinpoint colonies. However, the pinpoint colony isolates appeared to be more virulent in an in vivo challenge model in chickens than their normal-sized-colony counterparts. In addition, pinpoint morphology and associated slow growth were expressed without reversion after in vitro and in vivo passage, suggesting a genuine altered phenotype, and in some instances normal colonies converted to pinpoint morphology postinfection. In conclusion, small-colony variants of E. faecalis are described for the first time from veterinary clinical sources and in relation to amyloid arthropathy in chickens.
Extending the BLEU MT Evaluation Method with Frequency Weightings

We present the results of an experiment on extending the automatic method of Machine Translation evaluation BLUE with statistical weights for lexical items, such as tf.idf scores. We show that this extension gives additional information about evaluated texts; in particular it allows us to measure translation Adequacy, which, for statistical MT systems, is often overestimated by the baseline BLEU method. The proposed model uses a single human reference translation, which increases the usability of the proposed method for practical purposes. The model suggests a linguistic interpretation which relates frequency weights and human intuition about translation Adequacy and Fluency.
Androgenetic alopecia in children: report of 20 cases

Androgenetic alopecia (AGA) is the most common type of hair loss in adults. Although there are differences in the age at onset, the disease starts after puberty when enough testosterone is available to be transformed into dihydrotestosterone. We report 20 prepubertal children with AGA, 12 girls and eight boys, age range 6–10 years, observed over the last 4 years. All had normal physical development. Clinical examination showed hair loss with thinning and widening of the central parting of the scalp, both in boys and girls. In eight cases frontal accentuation and breach of frontal hairline were also present. The clinical diagnosis was confirmed by pull test, trichogram and dermoscopy in all cases, and by scalp biopsy performed in six cases. There was a strong family history of AGA in all patients. The onset of AGA is not expected to be seen in prepubertal patients without abnormal androgen levels. A common feature observed in our series of children with AGA was a strong genetic predisposition to the disease. Although the pathogenesis remains speculative, endocrine evaluation and a strict follow‐up are strongly recommended.
An Exact Method for Balancing Efficiency and Equity in the Liver Allocation Hierarchy

We study the problem of (re)designing the regional network by which cadaveric livers are allocated. Whereas prior research focused mainly on maximizing a measure of efficiency of the network that was based on aggregate patient survival, we explicitly account for the trade-off between efficiency and a measure of geographical equity in the allocation process. To this end, we extend earlier optimization models to incorporate both objectives and develop an exact branch-and-price approach to solve this problem, generalizing a solution approach studied for the case where only efficiency is taken into account. In addition, we propose an effective solution algorithm that approximates the (generally nonconcave) frontier of Pareto-efficient solutions with respect to the two objectives by simultaneously generating and successively improving upper and lower bounds on this frontier. We implement and test our approach on observed data and show that solutions significantly dominating the current configuration in both efficiency and equity can be found. Of course, other subjective criteria are needed to choose among the different Pareto-efficient candidate solutions.
Intergenic and Repeat Transcription in Human, Chimpanzee and Macaque Brains Measured by RNA-Seq

Transcription is the first step connecting genetic information with an organism's phenotype. While expression of annotated genes in the human brain has been characterized extensively, our knowledge about the scope and the conservation of transcripts located outside of the known genes' boundaries is limited. Here, we use high-throughput transcriptome sequencing (RNA-Seq) to characterize the total non-ribosomal transcriptome of human, chimpanzee, and rhesus macaque brain. In all species, only 20–28% of non-ribosomal transcripts correspond to annotated exons and 20–23% to introns. By contrast, transcripts originating within intronic and intergenic repetitive sequences constitute 40–48% of the total brain transcriptome. Notably, some repeat families show elevated transcription. In non-repetitive intergenic regions, we identify and characterize 1,093 distinct regions highly expressed in the human brain. These regions are conserved at the RNA expression level across primates studied and at the DNA sequence level across mammals. A large proportion of these transcripts (20%) represents 3′UTR extensions of known genes and may play roles in alternative microRNA-directed regulation. Finally, we show that while transcriptome divergence between species increases with evolutionary time, intergenic transcripts show more expression differences among species and exons show less. Our results show that many yet uncharacterized evolutionary conserved transcripts exist in the human brain. Some of these transcripts may play roles in transcriptional regulation and contribute to evolution of human-specific phenotypic traits.
Performance of an ELISA and Indirect Immunofluorescence Assay in Serological Diagnosis of Zoonotic Cutaneous Leishmaniasis in Iran

Serological assays have been extensively evaluated for diagnosis of visceral leishmaniasis (VL) and considered as a routine method for diagnosis of VL while these methods are not properly evaluated for diagnosis of cutaneous leishmaniasis (CL). This study aimed to assess the performance of indirect immunofluorescent-antibody test (IFA) and enzyme-linked immunosorbent assay (ELISA) for serodiagnosis of cutaneous leishmaniasis in Iran. Sixty-one sera samples from parasitologically confirmed CL patients and 50 sera from healthy controls along with 50 sera from non-CL patients were collected. Antigen was prepared from promastigotes and amastigotes of Leishmania major. IFA was used to detect anti-Leishmania IgG while ELISA was used to detect anti-Leishmania IgM, total IgG, or IgG subclasses (IgG1 and 4). ELISA, for detection of total IgG and IgM, showed sensitivity of 83.6% and 84.7% and specificity of 62.7% and 54.6%, respectively. Sensitivity and specificity of ELISA for detecting IgG1 and IgG4 were 64%, 75% and 85%, 49%, respectively. Sensitivity and specificity of IFA were 91.6% and 81%. Conclusion. Findings of this study demonstrated that serological test, especially IFA, can be used for proper diagnosis of CL.
Engineered Escherichia coli with Periplasmic Carbonic Anhydrase as a Biocatalyst for CO2 Sequestration

ABSTRACT Carbonic anhydrase is an enzyme that reversibly catalyzes the hydration of carbon dioxide (CO2). It has been suggested recently that this remarkably fast enzyme can be used for sequestration of CO2, a major greenhouse gas, making this a promising alternative for chemical CO2 mitigation. To promote the economical use of enzymes, we engineered the carbonic anhydrase from Neisseria gonorrhoeae (ngCA) in the periplasm of Escherichia coli, thereby creating a bacterial whole-cell catalyst. We then investigated the application of this system to CO2 sequestration by mineral carbonation, a process with the potential to store large quantities of CO2. ngCA was highly expressed in the periplasm of E. coli in a soluble form, and the recombinant bacterial cell displayed the distinct ability to hydrate CO2 compared with its cytoplasmic ngCA counterpart and previously reported whole-cell CA systems. The expression of ngCA in the periplasm of E. coli greatly accelerated the rate of calcium carbonate (CaCO3) formation and exerted a striking impact on the maximal amount of CaCO3 produced under conditions of relatively low pH. It was also shown that the thermal stability of the periplasmic enzyme was significantly improved. These results demonstrate that the engineered bacterial cell with periplasmic ngCA can successfully serve as an efficient biocatalyst for CO2 sequestration.