Miracle-dz/UniFAR-FTUs huggingface dataset:
Estimating the number of protein folds and families from complete genome data.

Using the data on proteins encoded in complete genomes, combined with a rigorous theory of the sampling process, we estimate the total number of protein folds and families, as well as the number of folds and families in each genome. The total number of folds in globular, water- soluble proteins is estimated at about 1000, with structural information currently available for about one-third of the number. The sequenced genomes of unicellular organisms encode from approximately 25%, for the minimal genomes of the Mycoplasmas, to 70-80% for larger genomes, such as Escherichia coli and yeast, of the total number of folds. The number of protein families with significant sequence conservation was estimated to be between 4000 and 7000, with structures available for about 20% of these.
Detailed phenotypic characterization of five temperature-sensitive mutants in the 22- and 147-kilodalton subunits of vaccinia virus DNA-dependent RNA polymerase

We have carried out detailed phenotypic characterization of five temperature-sensitive (ts) mutants of vaccinia virus, the ts lesions of which have previously been mapped to two different subunits of the viral RNA polymerase. We have also attempted to determine the mechanism of temperature sensitivity in these mutants. Phenotypic characterization of each of the mutants showed that at the nonpermissive temperature, all five mutants exhibited normal levels of early viral mRNA and protein synthesis, but for an extended period of time, all mutants accumulated normal levels of DNA in abnormally large pools in the cell cytoplasm; all mutants were defective in the synthesis of late viral mRNA and proteins and in viral morphogenesis. In an attempt to address the mechanism of temperature sensitivity in these mutants, we measured the effect of a temperature shift on the ability of the mutants to direct late viral protein synthesis. If infected cells were shifted down from a nonpermissive temperature late during infection, late protein synthesis was initiated after a lag period of 1 to 2 h. If infected cells were shifted up from a permissive temperature early during infection, late protein synthesis continued to be defective. If infected cells were shifted up to the nonpermissive temperature after late protein synthesis had commenced, late protein synthesis was maintained at the nonpermissive temperature at the level observed when the temperature was shifted up. We interpret these results to mean that once a functional RNA polymerase has been assembled at the permissive temperature during a mutant infection, it remains functional at the nonpermissive temperature, but that the ts mutants are defective in the assembly of a newly synthesized RNA polymerase at the nonpermissive temperature. This interpretation implies that the virion RNA polymerase is responsible for early viral transcription and that a newly synthesized RNA polymerase transcribes late viral genes.
Neoformation of boldenone and related steroids in faeces of veal calves

Abstract Conflicting findings regarding the boldenone content of bovine faeces suggest it may be synthesized de novo in emitted faeces. We tested this hypothesis by analysing uncontaminated urine, fresh and various forms of dried faeces from 10 calves (not given boldenone) by liquid chromatography/tandem mass spectrometry for 17α- and 17β-boldenone (α and β BOL); 1,4-androstadiene-3,17-dione (ADD); 4-androstene-3,17-dione (AED), testosterone (T) and epitestosterone (ET). Urine contained no α BOL, β BOL or ADD. The analysed substances were variably present in the rectal faeces, and at generally higher levels in faeces scraped from skin or stall floor. In pooled rectal faeces naturally dried for 13 days, α BOL, ADD, AED and ET levels were extremely high (much higher than accounted for by increases due to drying), and β BOL and T were absent. It is concluded that de novo synthesis of α BOL and metabolites occurs naturally in bovine faeces and only uncontaminated urine should be analysed for illegal boldenone.
Light induces programmed cell death by activating multiple independent proteases in a cone photoreceptor cell line.

PURPOSE Although the apoptotic death of photoreceptor cells in retinal degenerative disorders is well documented, the molecular mechanism is not understood. The objective of this study was to determine the molecular events leading to the death of photoreceptor cells. METHODS An assay was developed wherein 661W cells, a cone photoreceptor cell line, were stressed with light and percentage of surviving cells was determined. The degree of cell death was established using the MTT assay. Western blot analysis was used to confirm the activation of multiple proteases. Amounts of retinaldehydes were determined by extraction and HPLC. RESULTS 661W cells were more susceptible to light stress only in the presence of the chromophore 9-cis retinal for 4 hours. On exposure to light, 9-cis retinal was converted to all-trans retinal, which was found to be toxic to cells in the presence of light. However, all-trans retinol, which is the product of action by the enzyme retinol dehydrogenase on all-trans retinal, was not toxic. The sensitivity to light increased with serum deprivation. Light stress activated caspases, calpain 2, and cathepsin D independently and led to the demise of the cell. The mitochondria-dependent apoptotic pathway was also activated after the truncation of Bid, the pre-proapoptotic protein. Truncation of Bid led to the release of cytochrome c from the mitochondria and the activation of caspase 9. CONCLUSIONS The activation of multiple proteases by light-induced stress is a relevant finding for studies conducted to investigate the use of pharmaceutical agents to retard or cure the loss of cone photoreceptors observed in age-related macular degeneration and other degenerative retinal diseases.
Lack of microsatellite instability in neoplasms of ampulla of Vater

To clarify the genetic background of ampullary neoplasm, we investigated the occurrence of microsatellite instability (MSI) in 64 samples of neoplasm of the ampulla of Vater. Eight out of 22 adenomas (34.6%), nine out of 32 carcinomas (28.1%) and one metastatic lesion (10.0%) showed MSI in 1–3 of the nine dinucleotide markers; those cases are categorized into microsatellite instability‐low (MSI‐L). The remaining samples were stable with respect to all of the tested markers. None of the samples showed a frameshift mutation in the poly A‐tract of BAT‐26 or transforming growth factor‐β type II receptor, which are frequently mutated in gastric or colorectal cancers showing microsatellite instability. To confirm our finding, we stained 93 ampullary neoplasms with antibodies against the mismatch repair proteins: hMLH1 and hMSH2. All tumors were found to express mismatch repair proteins. In contrast to gastric or colorectal cancers, MSI does not play an important role in the carcinogenesis of ampullary carcinoma.
The Scale of Sexual Aggression in Southeast Asia: A Review

Southeast Asia is one of the most dynamic regions in the world. It is experiencing rapid socioeconomic change that may influence the level of sexual aggression, but data on the scale of sexual aggression in the region remain sparse. The aim of the present article was to systematically review the findings of studies available in English on the prevalence of self-reported sexual aggression and victimization among women and men above the age of 12 years in the 11 countries of Southeast Asia (Brunei, Cambodia, East Timor, Indonesia, Laos, Malaysia, Myanmar, the Philippines, Singapore, Thailand, and Vietnam). Based on four scientific databases, the search engine Google, Opengrey database, and reference checking, 49 studies were found on sexual victimization. Of those, 32 included only women. Self-reported perpetration was assessed by only three studies and included all-male samples. Prevalence rates varied widely across studies but showed that sexual victimization was widespread among different social groups, irrespective of sex and sexual orientation. Methodological heterogeneity, lack of representativeness of samples, imbalance of information available by country, missing information within studies, and cultural differences hampered the comparability between and within countries. There is a need for operationalizations that specifically address sexual aggression occurring after the age of consent, based on detailed behavioral descriptions of unwanted sexual experiences and allied to a qualitative approach with cultural sensitivity. Data on sexual aggression in conflict settings and in human trafficking are also limited. Recommendations for future research are presented in the discussion.
Does Dextrose Affect Analgesia or the Side Effects of Intrathecal Sufentanil?

Intrathecal (IT) sufentanil provides rapid effective pain relief for early labor, but it also produces undesirable side effects, which may be primarily related to cephalad spread.Although the combination of dextrose and positioning the patient head-up limits the spread of other spinally administered drugs, these factors have not been examined in laboring women receiving IT sufentanil. We hypothesized that the addition of dextrose to IT sufentanil injected with women in the sitting position would limit cephalad spread and side effects. Sixty-six healthy nulliparous parturients in early labor were randomized to receive 2-mL IT injections of sufentanil 10 micro g plus saline with patients in either the lateral decubitus or sitting position, sufentanil 10 micro g plus dextrose 7.5% with patients in either the lateral decubitus or sitting positions, or plain dextrose 7.5%. Pain scores using a 10-cm visual analog pain scale, sensory block height, and side effects were recorded. Dextrose 7.5% did not affect cephalad spread, as measured by block height to pin testing, but it did significantly reduce the duration of analgesia and the incidence of pruritus from IT sufentanil administered to patients in the sitting position compared with patients in the lateral position. In contrast, patient position had no effect on analgesia or side effects in patients receiving IT sufentanil in saline. IT dextrose alone had no effect. Implications: The authors conclude that the addition of dextrose to intrathecal sufentanil injected into patients in the sitting position reduces the duration of analgesia without significantly reducing side effects with the exception of pruritus, and therefore does not improve the clinical utility of intrathecal sufentanil. (Anesth Analg 1997;85:826-30)
A small predicted stem-loop structure mediates oocyte localization of Drosophila K10 mRNA.

The establishment of dorsoventral polarity in the Drosophila oocyte and future embryo is dependent on the efficient transport of K10 mRNA from nurse cells into the oocyte. To investigate the cis-requirements of K10 mRNA transport, we used a transgenic fly assay to analyze the expression patterns of a series of K10 deletion variants. Such studies identify a 44 nucleotide sequence within the K10 3' untranslated region that is required and sufficient for K10 mRNA transport and subsequent localization to the oocyte's anterior cortex. An inspection of the 44 nucleotide transport/localization sequence (TLS) reveals a strong potential for the formation of a stem-loop secondary structure. Nucleotide substitutions that interfere with the predicted base-pairing of the TLS block mRNA transport and anterior localization. Conversely, mutations that alter the base composition of the TLS while maintaining predicted base-pairing do not block mRNA transport or anterior localization. We conclude that K10 mRNA transport and anterior localization is mediated by a 44 nucleotide stem-loop structure. A similar putative stem-loop structure is found in the 3' untranslated region of the Drosophila orb mRNA, suggesting that the same factors mediate the transport and anterior localization of both K10 and orb mRNAs. Apart from orb, the K10 TLS is not found in any other localized mRNA, raising the possibility that the transport and localization of other mRNAs, e.g., bicoid, oskar and gurken, are mediated by novel sets of cis- and trans-acting factors. Moreover, we find that the K10 TLS overrides the activity of oskar cis-regulatory elements that mediate the late stage movement of the mRNA to the posterior pole. We propose the existence of a family of cis-regulatory elements that mediate mRNA transport into the oocyte, only some of which are compatible with the elements that mediate late stage movements.
Dominance of the E89G Substitution in HIV-1 Reverse Transcriptase in Regard to Increased Polymerase Processivity and Patterns of Pausing*

The substitution of a glycine for glutamic acid at position 89 in human immunodeficiency virus-1 (HIV-1) reverse transcriptase (RT) (E89G) confers resistance to several nucleoside and non-nucleoside inhibitors of RT. As residue 89 contacts the template strand, it has been suggested that this mutation may modulate the conformation of the RT·template/primer complex. In addition, certain mutations in RT that confer resistance to nucleoside analogs, such as M184V, are located near the polymerase active site. To characterize further these substitutions, we performed processivity assays alongside an analysis of pausing profiles with wild-type (wt) RT and recombinant RTs containing substitutions at E89G, M184V, or both. We now show that E89G RT has higher processivity than wt enzyme as well as a different pattern of pausing sites. Similar findings were obtained with the doubly mutated RT, although enzyme containing only the M184V mutation had lower processivity than wt. Consistent with these observations, and from a mechanistic standpoint, both E89G-containing as well as doubly mutated RT had decreased dissociation constants from a complex consisting of RT and template-primer, in comparison with either wt RT or M184V-containing RT. No significant differences were observed among the various enzymes in regard to K m values for the heteropolymeric RNA template used in these studies. Viruses containing the E89G mutation synthesized longer strand DNA products than either wt viruses or viruses containing only the M184V mutation in endogenous RT assays. Thus, the E89G substitution is a dominant determinant in regard to each of the k offvalues from an RT·template/primer complex, RT processivity, and specific patterns of pausing during DNA polymerization.
SURVEY OF AEROMONAS HYDROPHILA IN THREE MARINE FISH SPECIES FROM NORTH WEST ARABIAN GULF, IRAQ

This study preformed on 74 samples of marine water fishes (24 of Epinephelus tauvina , 27 of Hilsa ilisha and 23 of Lethriuns nebulosus ). Which collected from North West Arabian Gulf of Basrah. All samples were examined for the presence of Aeromonas hydrophila in muscles. 24 isolates of Aeromonas hydrophila were obtained, 8 (33.3%) from Epinephelus tauvina , 12 (44.4%) from Hilsa ilisha , and 4 (17.39%) from Lethriuns nebulosus . Then all isolates were examined for their ability to hemolytic activity as a virulence factor, the higher percentage of hemolytic activity isolates was found in Epinephelus tauvina .
Cultivation of cherry tomato under irrigation with saline water and nitrogen fertilization

The study was carried out from August 2013 to January 2014 to evaluate growth and production of cherry tomato cultivated under irrigation with water of different salinity levels and fertilized with different nitrogen (N) doses, in experiment conducted in drainage lysimeters under greenhouse conditions, at the Center for Agrifood Science and Technology of the Federal University of Campina Grande. The statistical design was randomized blocks in a 5 x 4 factorial scheme, with three replicates, and the treatments consisted of five levels of electrical conductivity of water (0.3, 1.5, 2.5, 3.5 and 4.5 dS m-1) and four N doses (60, 100, 140 and 180 mg kg-1). Growth and production variables of cherry tomato decrease linearly from the irrigation water salinity of 0.3 dS m-1 on. The longer exposure of plants to salt stress caused the highest reductions, and the root dry matter, leaf area and the number of clusters are the most sensitive variables. The highest value of plant height at 125 days after transplantation was obtained with the N dose of 139 mg kg-1 of soil. Increasing N doses reduced the effect of salinity on cherry tomato growth at 125 days after transplantation.
The Lifelong Impact of X-Linked Hypophosphatemia: Results From a Burden of Disease Survey

Abstract Context X-linked hypophosphatemia (XLH) is characterized by excess fibroblast growth factor 23 (FGF23), hypophosphatemia, skeletal abnormalities, and growth impairment. We aimed to understand the burden of disease of XLH across the lifespan. Methods Responses were collected from adults with XLH and parents/caregivers of a child with XLH in an online survey, including multiple-choice and open-ended questions on demographics, disease manifestations, treatment history, assistive device use, and age-specific patient-reported outcomes (PROs). Results Data were collected from 232 adults with XLH (mean age, 45.6 years; 76% female) and 90 parents/caregivers of a child with XLH (mean age, 9.1 years; 56% female). Mean age recalled for symptom onset was 3.2 years for adults and 1.3 years for children. When surveyed, nearly all children (99%) and 64% of adults were receiving oral phosphate, active vitamin D, or both. Prior participation in a trial investigating burosumab, a fully human monoclonal antibody against FGF23, was reported in 3% of children and 10% of adults; of these respondents, only one child reported current treatment with burosumab at the time of the survey. Both children and adults reported typical features of XLH, including abnormal gait (84% and 86%, respectively), bowing of the tibia/fibula (72% and 77%), and short stature (80% and 86%). Nearly all adults (97%) and children (80%) reported bone or joint pain/stiffness. Adults reported a history of fractures (n/N = 102/232; 44%), with a mean (SD) age at first fracture of 26 (16) years. Adults reported osteophytes (46%), enthesopathy (27%), and spinal stenosis (19%). Mean scores for PROs evaluating pain, stiffness, and physical function were worse than population norms. Analgesics were taken at least once a week by 67% of adults. Conclusions Despite the common use of oral phosphate and active vitamin D established in the 1980s, children with XLH demonstrate a substantial disease burden, including pain and impaired physical functioning that persists, as demonstrated by similar responses reported in adults with XLH.
Computer-assisted knee arthroplasty is better than a conventional jig-based technique in terms of component alignment.

Intervention: Patients were allocated to CAKA (n = 34) or conventional jig-based knee arthroplasty (JBKA) (n = 36). CAKA was done using the Stryker Knee Navigation system (Stryker, Kalamazoo, Michigan), which makes use of anatomical mapping of the knee and kinematic analysis of the limb to make a working model of the knee, and an infrared camera to track and relate the position of a pointer or attachment to the mapped anatomy shown in real time on a computer screen. JBKA was done with use of intramedullary instrumentation for the femur and extramedullary instrumentation for the tibia.
Adherencia y cumplimiento del método anticonceptivo hormonal oral

Objetivo: Identificar los factores relacionados con la adherencia y el cumplimiento de las mujeres con los anticonceptivos hormonales orales (ACO). Metodologia: Revision bibliografica. Se realizo una busqueda en las bases de datos PubMed, CINAHL, Cochrane Library, MEDES y ENFISPO en los ultimos 10 anos. Resultados: Se seleccionaron un total de 35 articulos originales y una revision bibliografica. Los factores que mejoran el cumplimiento de los ACO son los conocimientos que tiene la mujer sobre la pildora, iniciar el metodo de forma inmediata y el apoyo de la pareja. Los factores que influyen en la adherencia son el coste de los ACO, la falta de conocimientos ante los olvidos y la practica de descansos de la pildora. Conclusiones: El consejo contraceptivo debe ser individualizado, teniendo en cuenta los factores que afectan a la adherencia y el cumplimiento.
Dystrophic Serotonin Axons in Postmortem Brains from Young Autism Patients

Autism causes neuropathological changes in varied anatomical loci. A coherent neural mechanism to explain the spectrum of autistic symptomatology has not been proposed because most anatomical researchers focus on point‐to‐point functional neural systems (e.g., auditory and social networks) rather than considering global chemical neural systems. Serotonergic neurons have a global innervation pattern. Disorders Research Program, AS073234, Program Project (JW). Their cell bodies are found in the midbrain but they project their axons throughout the neural axis beginning in the fetal brain. This global system is implicated in autism by animal models and by biochemical, imaging, pharmacological, and genetics studies. However, no anatomical studies of the 5‐HT innervation of autistic donors have been reported. Our review presents immunocytochemical evidence of an increase in 5‐HT axons in postmortem brain tissue from autism donors aged 2.8–29 years relative to controls. This increase is observed in the principle ascending fiber bundles of the medial and lateral forebrain bundles, and in the innervation density of the amygdala and the piriform, superior temporal, and parahippocampal cortices. In autistic donors 8 years of age and up, several types of dystrophic 5‐HT axons were seen in the termination fields. One class of these dystrophic axons, the thick heavily stained axons, was not seen in the brains of patients with neurodegenerative diseases. These findings provide morphological evidence for the involvement of serotonin neurons in the early etiology of autism, and suggest new therapies may be effective to blunt serotonin's trophic actions during early brain development in children. Anat Rec, 2011. © 2011 Wiley‐Liss, Inc.
Implications for the neural basis of social cognition for the study of schizophrenia.

OBJECTIVE The study of social cognition in schizophrenia has received growing attention in recent years. At the same time, a large body of work has explored the neural basis of social cognition in both nonclinical and clinical groups, other than those with schizophrenia. The gap between these two literatures is considerable and may slow progress in creating a comprehensive social cognitive model of schizophrenia. This article attempts to bridge this gap by discussing how the neural basis of social cognition may inform future clinical research in schizophrenia. METHOD PsycINFO and MEDLINE were systematically searched for articles pertaining to the neural basis of social cognition and social cognition in schizophrenia. Relevant studies were obtained and synthesized into a comprehensive review and integrative formulation. RESULTS Striking parallels between these two areas of research were found. CONCLUSIONS These parallels might help to better elucidate the underlying mechanisms for social cognitive and social behavioral impairments in schizophrenia as well as provide potential targets for treatment and drug development.
The prevalence and outcome of depression and dementia in Botany's elderly population

Large epidemiological studies of adult populations have reported depression to be less prevalent in old age than among younger adults, whereas studies limited to older persons have reported rates that vary considerably, some showing high rates of depression. There was, therefore, reason to check data from a study that reported high rates, and to review evidence in relation to diagnosis and outcome.