Miracle-dz/UniFAR-FTUs huggingface dataset:
Genome Sequence of the Piezophilic, Mesophilic Sulfate-Reducing Bacterium Desulfovibrio indicus J2T

ABSTRACT The complete genome sequence of Desulfovibrio indicus J2T, a member of the family Desulfovibrionaceae, consists of 3,966,573-bp in one contig and encodes 3,461 predicted genes, 5 noncoding RNAs, 3 rRNAs operons, and 52 tRNA-encoding genes. The genome is consistent with a heterotrophic, anaerobic lifestyle including the sulfate reduction pathway.
Prevalence of dementia in the city of Helsinki

The Helsinki Aging Study is based on a random sample of 795 subjects aged 75‐years (N = 274), 80‐years (N = 266) and 85‐years (N = 255). A clinical examination including Clinical Dementia Rating (CDR)‐scale was carried out in 82% of the cases. 93 demented subjects were found, 17 of whom had mild dementia. The prevalence of moderate and severe dementia was 2.9%, 10.3% and 23.3% in the age groups of 75‐year‐olds, 80‐year‐olds and 85‐year‐olds, respectively. If we take into account also the mild cases, we get the prevalence of dementia 4.6%, 13.1% and 26.7% in the above mentioned age groups, respectively. The proportion of mild dementias was lower than expected, which probably reflects both the difficulties to recognize mild dementia in an elderly population and the relatively small compensatory capacity of elderly people.
Chlamydial infections of the cervix.

A major problem in the control of non-specific genital infection (NSGI) is the difficulty of identifying the disease in women. In men, non-specific urethritis (NSU) is diagnosed when there are significant numbers of polymorphonuclear leucocytes in urethral secretions, certain known causes of urethritis such as N. gonorrhoeae having been excluded. This approach is not possible in women. Polymorphonuclear leucocytes are present in the lower genital tract in many women, so that their enumeration has little diagnostic significance, and the value of clinical or cytological evidence of cervical inflammation is unproved. The only women likely to be suspected of having NSGI are those who have sexual contacts with NSU, and these women may receive a course of treatment; women who are unaware that they have a sexual contact who has NSU are likely to remain undiagnosed. The identification and treatment of women with NSGI will be difficult until the infecting organism or organisms can be demonstrated. Evidence has now accumulated which indicates that organisms of Chlamydia Group A may cause many infections of NSU. By the use of a sensitive cell culture system it has been shown that Chlamydia can be isolated from about 40 per cent. of men with NSU (Dunlop, Vaughan-Jackson, Darougar, and Jones, 1972; Oriel, Reeve, Powis, Miller, and Nicol, 1972). The organisms have also been found in 25 to 30 per cent. of men with gonococcal urethritis, and these men may be particularly liable to develop postgonococcal urethritis (Richmond, Hilton, and Clarke, 1972; Powis, Oriel, and Reeve, 1973). Chlamydia is rarely found in men who do Inot have urethritis (Oriel and others, 1972). Some recent observations indicate that chlamydial infection of the urethra may be accompanied by significant, and sometimes rising, titres of chlamydial antibodies, detected by immunofluorescent and radio-immune precipitation techniques (Reeve, Gerloff, Casper, Philip, Oriel, and Powis, 1974). Although direct proof cannot be obtained in the absence of experiments using human
Monoallelic BUB1B mutations and defective mitotic‐spindle checkpoint in seven families with premature chromatid separation (PCS) syndrome

Cancer‐prone syndrome of premature chromatid separation (PCS syndrome) with mosaic variegated aneuploidy (MVA) is a rare autosomal recessive disorder characterized by growth retardation, microcephaly, childhood cancer, premature chromatid separation of all chromosomes, and mosaicism for various trisomies and monosomies. Biallelic BUB1B mutations were recently reported in five of eight families with MVA syndrome (probably identical to the PCS syndrome). We here describe molecular analysis of BUB1B (encoding BubR1) in seven Japanese families with the PCS syndrome. Monoallelic BUB1B mutations were found in all seven families studied: a single‐base deletion (1833delT) in four families; and a splice site mutation, a nonsense mutation, and a missense mutation in one family each. Transcripts derived from the patients with the 1833delT mutation and the splice site mutation were significantly reduced, probably due to nonsense‐mediated mRNA decay. No mutation was found in the second alleles in the seven families studied, but RT‐PCR of BUB1B and Western blot analysis of BubR1 indicated a modest decrease of their transcripts. BubR1 in the cells from two patients showed both reduced protein expression and diminished kinetochore localization. Their expression level of p55cdc, a specific activator of anaphase‐promoting complex, was normal but its kinetochore association was abolished. Microcell‐mediated transfer of chromosome 15 (containing BUB1B) into the cells restored normal BubR1 levels, kinetochore localization of p55cdc, and the normal responses to colcemid treatment. These findings indicate the involvement of BubR1 in p55cdc‐mediated mitotic checkpoint signaling, and suggest that >50% decrease in expression (or activity) of BubR1 is involved in the PCS syndrome. © 2006 Wiley‐Liss, Inc.
Dendritic cells with antigen-presenting capability reside in airway epithelium, lung parenchyma, and visceral pleura

In this study, we identified a population of dendritic cells (DC) that exists throughout human and mouse pulmonary tissues, including the trachea, bronchi, alveoli, and visceral pleura. In human tissue, these DC were shown to be positive for HLA-DR and T200 antigens. In the mouse, the DC expressed not only Ia and the T200 antigen, but also Fc- IgG and C3bi receptors. Unlike alveolar macrophages, the DC were negative for nonspecific esterase staining and shared ultrastructural similarities with the DC described by Steinman (1), and with Langerhans' cells, even though they did not contain Birbeck granules. We were able to demonstrate that mouse pulmonary DC function in antigen presentation, as observed with the other DC. Thus, the respiratory tract contains DC that are capable of functioning in antigen presentation and that may be important in pulmonary immune responses.
Analysis of Synonymous Codon Usage in the Capsid Gene UL38 of Duck Enteritis Virus

In the study, we calculated the codon usage bias in the newly identified UL38 gene of Duck Enteritis Virus (DEV) and performed a correlation analysis of codon bias of DEV UL38 gene and its host animal. There was a strong bias in the DEV UL38 gene towards the synonymous codons with A and T at the third codon position. The amino acids codon usage bias in the DEV UL38 gene was compared with other 15 reference herpesviruses, and the cluster analysis suggested that UL38 gene's type and function also contributed to the codon usage of it. In addition, there were 42 rare condons in the ORF of the DEV UL38, and 24 codons showing distinct usage differences between DEV and E. coli, 12 codons between DEV and Homo sapiens, 25 codons between DEV and yeast.
Effect of polymer host on third order nonlinear optical properties of newly synthesized organic liquid crystal

We report the investigation of third order optical nonlinearity of 2,4,6-tri-(p-hyptoyoxylphenyl) pyrilium tetraborate doped PMMA using nanosecond laser pulses at 532 nm wavelength by employing Z-Scan technique. To see the effect of polymer host, the results have been compared with the pure dopant. The material shows a large negative nonlinearity with real and imaginary parts of chi(3) are - 3.31times10-14 esu and 0.73times10-14 esu respectively. Excited state absorption cross-section is found to be 3.41times10-48 cm4.s/photon in PMMA host. The magnitude of third order nonlinear parameters increases when the compound is doped into PMMA matrix because of change in the conformation of chain geometry as a result of charge transfer processes. The values are comparable with a best known nonlinear liquid crystal molecule namely, 4-cyano-4'-n-pentylbiphenyl in the nematic phase. Hence, these molecules can be suitably used as nonlinear optical materials in PMMA matrix for device applications.
Practice of Epidemiology Validation of Pediatric Diabetes Case Identification Approaches for Diagnosed Cases by Using Information in the Electronic Health Records of a Large Integrated Managed Health Care Organization

We explored the utility of different algorithms for diabetes case identification by using electronic health records. Inpatient and outpatient diagnosis codes, as well as data on laboratory results and dispensing of antidiabetic medications were extracted from electronic health records of Kaiser Permanente Southern California members who were less than 20 years of age in 2009. Diabetes cases were ascertained by using the SEARCH for Diabetes in Youth Study protocol and comprised the “ gold standard. ” Sensitivity, specificity, positive and negative predictive values, accuracy, and the area under the receiver operating characteristic curve (AUC) were compared in 1,000 bootstrapped samples. Based on data from 792,992 youth, of whom 1,568 had diabetes (77.2%, type 1 diabetes; 22.2%, type 2 diabetes; 0.6%, other), case identification accuracy was highest in 75% of bootstrapped samples for those who had 1 or more outpatient diabetes diagnoses or 1 or more insulin prescriptions (sensitivity, 95.9%; positive predictive value, 95.5%; AUC, 97.9%) and in 25% of samples for those who had 2 or more outpatient diabetes diagnoses and 1 or more antidiabetic medications (sensitivity, 92.4%; positive predictive value, 98.4%; AUC, 96.2%). Having 1 or more outpatient type 1 diabetes diagnoses ( International Classification of Diseases, Ninth Revision, Clinical Modification, code 250.x1
DoDOM: Leveraging DOM Invariants for Web 2.0 Application Reliability

Web 2.0 applications are increasing in popularity and are being widely adopted. However, they are prone to errors due to their non-deterministic behavior and the lack of error-detection mechanisms on the client side. This paper presents DoDOM, an automated system for detecting errors in a Web 2.0 application using dynamic analysis. DoDOM repeatedly executes the application under a given sequence of user actions and observes its behavior. Based on the observations, DoDOM extracts a set of invariants on the web application’s DOM structure. We show that invariants exist for real applications and can be learned within a reasonable number of executions. We further demonstrate the use of the invariants in detecting errors in web applications due to failures of events and the unavailability of domains.
C/EBPα is required for differentiation of white, but not brown, adipose tissue

The transcription factor CCAAT enhancer binding protein α (C/EBPα) is expressed at high levels in liver and adipose tissue. Cell culture studies show that C/EBPα is sufficient to trigger differentiation of preadipocytes into mature adipocytes, suggesting a central role for C/EBPα in the development of adipose tissue. C/EBPα knockout mice die within 7–12 h after birth. Defective gluconeogenesis of the liver and subsequent hypoglycemia contribute to the early death of these animals. This short life span impairs investigation of the development of adipose tissue in these mice. To improve the survival of C/EBPα−/− animals, we generated a transgenic line that expresses C/EBPα under the control of the albumin enhancer/promoter. This line was bred into the knockout strain to generate animals that express C/EBPα in the liver but in no other tissue. The presence of the transgene improved survival of C/EBPα−/− animals almost 3-fold. Transgenic C/EBPα−/− animals at 7 days of age show an absence of s.c. , perirenal, and epididymal white fat despite excess lipid substrate in the serum, whereas brown adipose tissue is somewhat hypertrophied and shows minimal biochemical alterations. Interestingly, mammary gland fat tissue is present and exhibits normal morphology. The absence of white adipose tissue in many depots in the presence of high serum lipid levels shows that C/EBPα is required for the in vivo development of this tissue. In contrast, brown adipose tissue differentiation is independent of C/EBPα expression. The presence of lipid in brown adipose tissue serves as an internal nutritional control, indicating that neither nutritional intake nor lipoprotein composition is likely responsible for the absence of white fat.
Effectiveness and cost‐effectiveness of paediatric bariatric surgery: a systematic review

Strong evidence for successful and cost‐effective obesity management strategies is still generally lacking, leading the medical profession to rely increasingly on surgical options to treat obesity in children and adolescents. We performed a systematic review to examine the effectiveness of surgical interventions to treat obese children and adolescents, and whether they are cost‐effective. We searched PubMed, ISI Web of Science, Embase and the Cochrane Library to 6 September 2010, and hand‐searched bibliographies. We included articles with English abstracts if they examined subjects ≤19 years of age, reported at least one postoperative weight loss measure and at least 1 year of postoperative follow‐up. Thirty‐seven relevant papers on bariatric surgery effectiveness in 831 children or adolescents were included, spanning 36 years. Thirteen studies examined gastric banding, with mean body mass index (BMI) reductions ranging from 8.5 to 43 kg m−2. Weight gain was reported in one case study. Eight papers examined Roux‐en‐Y gastric bypass, with mean BMI reductions ranging from 9 to 25 kg m−2. Fourteen publications studied other forms of bariatric surgery: sleeve gastrectomies, vertical banded gastroplasty, biliopancreatic diversion or a combination of procedures. Mean BMI reductions ranged from 9 to 24 kg m−2. Three surgery‐related mortalities were reported, as was weight regain in several cases. The majority of studies reported resolution or improvement of comorbid conditions. A range of postoperative complications were identified across surgery types, including: ulcers, intestinal leakage, wound infection, anastomotic stricture, nutritional deficiencies, bowel obstruction, pulmonary embolism, disrupted staple lines, band slippage, psychological intolerance and repeated vomiting. Evidence on cost‐effectiveness was limited to one Australian modelling project, which deemed laparoscopic adjustable gastric banding cost‐effective for adolescents. Existing evidence – although based generally on underpowered, retrospective studies – suggests that bariatric surgery in older children results in significant weight loss and improvements in comorbidities and quality of life. However, postoperative complications, compliance and follow‐up may be more problematic in adolescents than adults, and availability of long‐term data on safety, effectiveness and cost‐effectiveness remains largely unknown. Pending an improvement in the quality of available evidence, a cautious approach to child and adolescent bariatric surgery is warranted, and reversible techniques are advisable compared to approaches that permanently alter anatomy.
A stochastic proximal point algorithm for total variation regularization over large scale graphs

The total-variation (TV) regularizer is often used to promote the structured sparsity of a given real function over the vertices of a non-directed graph. Indeed, the proximity operator associated with TV regularizer promotes sparsity of the function discrete gradient. Although quite affordable in the special case of one-dimensional (1D) graphs, the computation of the proximity operator for general large scale graphs can be demanding. In this paper, we propose a stochastic algorithm for solving this problem over large graphs with a moderate iteration complexity. The algorithm consists in properly selecting random paths in the graph and computing 1D-proximity operators over these paths. Convergence of the algorithm is related to recent results on stochastic proximal point algorithms.
A Hardware Interface for Hashing Algorithms

The submissions to the SHA-3 competition include a reference implementation in C, built on top of a standard programmer's interface (API). This greatly improves the evaluation process: it enables portability across platforms, and it makes performance comparison of the algorithms easy. For hardware crypto-implementations, such a standard interface does not exist. As a result, the evaluation and comparison of hardware hashing algorithms becomes complex and error prone. The first step to improve the evaluation process for hardware is the definition of an interface. This document describes a general hardware interface for hashing algorithms. The operation of the interface is discussed, and the appendix lists a SHA-256 reference implementation that uses the interface.
CHARACTERIZATION OF SALMON (ONCORHYNCHUS KETA) AND STURGEON (ACIPENSER TRANSMONTANUS) CAVIAR PROTEINS

The solubility of protein components in salmon (Oncorhynchus keta) and sturgeon (Acipenser transmontanus) caviar in distilled water, 5% (w/v) NaCl, 70% (v/v) ethanol at 65C, and 0.2% (w/v) NaOH was determined. The salt soluble proteins were the predominant fraction and constituted 84.2% of the recovered protein in salmon and 86.1% in sturgeon samples. The two most prominent protein fractions (12.5% sodium dodecyl sulfate-polyacrylamide gel electrophoresis) for sturgeon caviar are most likely vitellin (96 kDa) and ovomucoid or phosvitin (28 kDa). For salmon roe, small proteins, possibly lysozyme or phosvitin (10 kDa), are also present.
Mapping of Rhodopseudomonas capsulata nif genes

The endogenous gene transfer system of Rhodopseudomonas capsulata was used to analyze mutations which block the ability to use molecular nitrogen as the sole nitrogen source (nif). With this fine-structure mapping tool, linkage of nif mutations could be reliably established if separated by 2,700 base pairs or less. Eleven independent mutations were analyzed, and five linkage groups were found. The overall chromosomal arrangement of these groups awaits conjugational or physical analysis. A candidate for the inactive subunit of R. capsulata Fe protein was located in gels at a position of about 38,000 molecular weight, 5,000 more than that of the presumed active subunit.
Cytochrome P450 detection in liver of the catfish Ancistrus multispinis (Osteichthyes, Loricariidae)

Respostas biologicas sensiveis aos contaminantes ambientais sao uteis para prever efeitos prejudiciais devido a exposicoes cronicas. Padronizacao de protocolos para quantificar parâmetros bioquimicos em diferentes especies de peixes e necessaria para validar o uso como biomarcador. Estudos comparativos de diferentes especies de peixe e sua interpretacao sao um avanco para a validacao do uso de biomarcadores gerais, representativos do impacto ambiental. Neste estudo o protocolo para a analise do citocromo P450 (CYP) do peixe nativo brasileiro Ancistrus multispinis foi estabelecido. Cyp e um biomarcador de exposicao principalmente de hidrocarbonetos policiclicos aromaticos (HAP), bifenilas policloradas (PCB) e dioxinas. A contaminacao do microssomo pela hemoglobina durante as analises do CYP no figado foi detectada, levando a uma interpretacao erronea dos resultados. O metodo espectrofotometrico para analise do CYP foi adaptado para diminuir a interferencia da hemoglobina. Alem disso, o metodo de western blotting para analise de CYP1A foi testado com sucesso para essa especie de peixe.
Improving health outcomes among individuals with HIV, mental illness, and substance use disorders in the Southeast

Abstract Providing behavioral treatment for mental health and substance use disorders among HIV-infected individuals is critical because these disorders have been associated with negative outcomes such as poorer medication adherence. This study examines the effectiveness of an integrated treatment model for HIV-infected individuals who have both substance use and mental disorders. Study participants (n = 141) were recruited through routine mental health and substance abuse screening at tertiary Infectious Disease clinics in North Carolina. The study participants received integrated mental health and substance abuse treatment for one year and were interviewed at three-month intervals. Using linear regression analyses, we detected statistically significant decreases in participants’ psychiatric symptomatology, illicit substance use, alcohol use, and inpatient hospital days. Participants also reported fewer emergency room visits and were more likely to be receiving antiretroviral medications and adequate psychotropic medication regimens at follow-up. No changes in sexual risk, physical health, or medical adherence were detected after treatment participation. This integrated treatment model offers an option for treating HIV-infected individuals with mental health and substance use disorders that can be adapted for use in a variety of psychiatric and medical treatment settings.
Colletotrichum incanum sp. nov., a curved-conidial species causing soybean anthracnose in USA

Soybean anthracnose is caused by a number of species of Colletotrichum that as a group represent an important disease that results in significant economic losses. In the current study, Colletotrichum species were isolated from soybean petioles and stems with anthracnose symptoms from soybean fields in Illinois. Multigene sequence phylogenic analysis, combining rDNA internal transcribed spacer, actin, β-tubulin, glyceraldehyde-3-phosphate dehydrogenase and histone H3 gene regions, revealed a group of isolates collected in this study to be distinct from other established Colletotrichum species. This new group was phylogenetically closer to C. liriopes, C. tofieldiae and C. verruculosum than to C. truncatum, another species with curved conidia commonly found on soybean. A representative isolate from this new group was used to examine its morphology, cultural characteristics and pathogenicity to soybean; it was found to differ from C. truncatum in colony culture characteristics and sizes of conidia and appressoria. As a result of the molecular phylogenetic, morphological and pathogenicity analyses, we named this species Colletotrichum incanum. Of the 84 Colletotrichum isolates collected from soybean petioles, 40 were C. incanum, indicating that this species may commonly occur.
Alternative RNA splicing that is spatially regulated: generation of transcripts from the Antennapedia gene of Drosophila melanogaster with different protein-coding regions

We have shown previously that transcription of the Drosophila homeotic gene Antennapedia results in four major RNA species which differ in long 5'- and 3'-untranslated sequences. The protein-coding portion of these transcripts, however, is located in exons common to all. Using RNase protection assays and further cDNA clone isolation, we have now detected two alternative splicing events between exons of this region. These result in four RNA variations which, if translated, would encode a family of Antennapedia proteins. By analyzing transcripts from various developmental stages and isolated tissues, we show that alternative splicing is under strict temporal and spatial regulation. For example, while similar patterns of splicing were found for all wild-type thoracic imaginal disks examined, these differed distinctly from the patterns observed in neural tissues. Our results suggest that individual RNAs may be associated with different biological roles, and provide molecular evidence that the Antennapedia gene is involved in multiple functions.