Miracle-dz/UniFAR-FTUs huggingface dataset:
Mortality associated with wines, beers, and spirits

Australian data suggest that choice of beverage relates to lifestyle and personality EDITOR,--Morten Gronbaek and colleagues suggest that mortality is lower in association with a moderate intake of wine, unchanged in association with a moderate intake of beer, and increased in association with a moderate intake of spirits.1 In their study they used a different reference group of subjects for each beverage considered--a group comprising teetotallers and beer and wine drinkers for the spirits comparison and a group comprising teetotallers and spirits and beer drinkers for the wine comparison--which makes the findings difficult to interpret. More importantly, they consider that confounders are unlikely to explain their results. In a group of working men in Western Australia, …
The integration host factor (IHF) integrates stationary‐phase and virulence gene expression in Salmonella enterica serovar Typhimurium

The integration host factor (IHF) is a DNA‐binding and ‐bending protein with roles in local DNA structural organization and transcriptional regulation in Gram‐negative bacteria. This heterodimeric protein is composed of the two highly homologous subunits IHFα and IHFβ. DNA microarray analysis was used to define the regulon of genes subject to IHF control in Salmonella enterica serovar Typhimurium (S. Typhimurium). The transcription profile of the wild type was compared with those of mutants deficient in IHFα, IHFβ, or both IHFα and IHFβ. Our data reveal a new connection between IHF and the expression of genes required by the bacterium to undergo the physiological changes associated with the transition from exponential growth to stationary phase. When a mutant lacking IHF entered stationary phase, it displayed downregulated expression of classic stationary‐phase genes in the absence of any concomitant change in expression of the RpoS sigma factor. Purified IHF was found to bind to the regulatory regions of stationary‐phase genes indicating an auxiliary and direct role for IHF in RpoS‐dependent gene activation. Loss of IHF also had a profound influence on expression of the major virulence genes and epithelial cell invasion, indicating a role in co‐ordinating regulation of the pathogenic traits with adaptation to stationary phase. Although the three mutants showed considerable overlaps in the genes affected by the ihf lesions, the observed patterns were not identical, showing that S. Typhimurium has not one but three overlapping IHF regulons.
Long-wavelength monolithic GaInNAs vertical-cavity optical amplifiers

We report on the continuous-wave amplification characteristics of an optically pumped 1.3-/spl mu/m multiple-quantum-well GaInNAs-GaAs vertical-cavity semiconductor optical amplifier (VCSOA). The VCSOA structure was monolithically grown by molecular beam epitaxy and operated in reflection mode in a fiber-coupled system. The maximum on-chip gain attained, limited by the onset of laser action, was 15.6 dB at 196 mW of 980-nm pump power. For a chip gain of 10.4 dB, the optical bandwidth was 10.8 GHz and the saturation output power was -9 dBm. By varying the pump laser power, a maximum extinction ratio of 22.3 dB was obtained. Temperature-controlled tuneable operation of the device is also presented and demonstration of 9 dB of chip gain obtained over 9.5 nm with an optical bandwidth of 12 GHz is reported.
Machine learning model for early detection of higher education students that need additional attention in introductory programming courses

Not all higher education students who enroll in introductory programming course successfully finish it, in particular if their major is not computer programming or computer science. From empirical evidence collected at the University College Algebra we have concluded that such students can be given a better passing chance if they are identified early in the semester and given additional attention in form of extra hours in classroom, guided by mentors. The challenge lies in being able to distinguish such students as early as possible so they can benefit from additional learning hours before the final exams. This paper proposes one such possible criterion: we develop a machine learning model based on previous generations of students and use it for current students to calculate the probability of finishing the course unsuccessfully. Such students are then classified as "requiring extra attention".
Plasma levels of endothelin‐1 after a pulmonary embolism of bone marrow fat

Background: During orthopedic surgery, embolization of bone marrow fat can lead to potentially fatal, intra‐operative cardiovascular deterioration. Vasoactive mediators may also be released from the bone marrow and contribute to these changes. Increased plasma levels of endothelin‐1 (ET‐1) have been observed after pulmonary air and thrombo‐embolism. The role of ET‐1 in the development of acute cardiovascular deterioration as a result of bone marrow fat embolization during vertebroplasty was therefore investigated.
Experimental and Computational Active Site Mapping as a Starting Point to Fragment‐Based Lead Discovery

Small highly soluble probe molecules such as aniline, urea, N‐methylurea, 2‐bromoacetate, 1,2‐propanediol, nitrous oxide, benzamidine, and phenol were soaked into crystals of various proteins to map their binding pockets and to detect hot spots of binding with respect to hydrophobic and hydrophilic properties. The selected probe molecules were first tested at the zinc protease thermolysin. They were then applied to a wider range of proteins such as protein kinase A, D‐xylose isomerase, 4‐diphosphocytidyl‐2C‐methyl‐D‐erythritol synthase, endothiapepsin, and secreted aspartic protease 2. The crystal structures obtained clearly show that the probe molecules populate the protein binding pockets in an ordered fashion. The thus characterized, experimentally observed hot spots of binding were subjected to computational active site mapping using HotspotsX. This approach uses knowledge‐based pair potentials to detect favorable binding positions for various atom types. Good agreement between the in silico hot spot predictions and the experimentally observed positions of the polar hydrogen bond forming functional groups and hydrophobic portions was obtained. Finally, we compared the observed poses of the small‐molecule probes with those of much larger structurally related ligands. They coincide remarkably well with the larger ligands, considering their spatial orientation and the experienced interaction patterns. This observation confirms the fundamental hypothesis of fragment‐based lead discovery: that binding poses, even of very small molecular probes, do not significantly deviate or move once a ligand is grown further into the binding site. This underscores the fact that these probes populate given hot spots and can be regarded as relevant seeds for further design.
Depressive Symptoms and Type 2 Diabetes Mellitus in Rural Appalachia: an 18-Month Follow-Up Study*

Objective Despite high rates of diabetes and depression in rural areas, limited data exists to document patterns and predictors of depressive symptoms in rural patients with type 2 diabetes (T2DM). The purpose of this study was to assess the rates and predictors of co-morbid depressive symptoms over an 18-month period in a cohort of rural Appalachian adults with T2DM. Methods N = 100 adult T2DM patients were recruited from family medicine and endocrinology practices located in the rural Appalachian counties of southeastern Ohio and West Virginia. Data were collected using a longitudinal observational survey design. Results The sample consisted of predominantly White (93%) females (62%) who were married (71%), completed high school or less (48%), and had a mean age of 60 years (SD 11). Mean BDI score was 14.0 (SD 12) with 27% scoring in the moderate/severe range for depressive symptoms. A majority of patients (77%) reported depressive symptoms, at both time points, with 88% of these reporting consistent depressive symptoms in the year prior to study follow-up. Patients with depressive symptoms at Time 1 and Time 2 did not differ from other groups in the number of treatment strategies or medications used. Predictors of depressive symptoms in this group were increased diabetes treatment complexity (OR = 2.3), lack of home ownership (OR = 11.4), and decreased satisfaction with antidepressant medications (OR = 2.0; χ2 = 28.9, p < .0001). Conclusions Rural T2DM patients reported high rates of repeated depressive symptoms without corresponding rates of depression treatment. These patients may benefit from close monitoring and ongoing adjustment of their treatment for depression and diabetes by primary care providers.
Complementary Use of NMR to X-Ray Crystallography for the Analysis of Protein Morphological Change in Solution

A vast amount of protein structure data is going to pave new ways in protein structure research. They improved the quality of predicted protein structure from its primary sequence (Sanchez and Sali 2000). The possible protein interaction sites to small ligand and/or the other proteins could be predicted based on the protein complex structures in the Protein Data Bank (PDB) (Morris et al. 2009). The combined use of bioinformatics with the protein structure data has been frequently giving invaluable outcomes to facilitate the understanding on the experimental results in biochemistry and molecular biology. In silico protein structure analyses are now already essential approaches in protein research. Protein structural data, most of which came from X-ray crystallography, are also useful to expand the protein structure analysis in solution, when combined with NMR. NMR chemical shift perturbation of a protein caused by the interaction with a compound, for example, allows sensitive identification of the interaction sites on protein (Shuker et al. 1996). This NMR derived binding site information with the protein structure facilitates drug design (Hajduk et al. 1997). This chemical shift-based approach is also applied to the protein-protein interaction, which enables to build a model protein complex structure (de Vries, van Dijk and Bonvin 2010, Dominguez, Boelens and Bonvin 2003). Although these approaches are now prevailingly used, there are limitations in their application. The approaches assume that the target protein retains the X-ray structure in solution and also negates the possible structural change caused by binding to a compound or a partner protein. Some of the proteins are known to have different domain arrangement from those in crystal (Skrynnikov et al. 2000a); it is often the case for the protein having domains linked by flexible linker. In addition, it is commonly found that proteins show structural change in response to compound binding or interaction with the other protein (Evenas et al. 2001). To expand the utility of protein structure data in the PDB in solution protein science, we need new NMR techniques to overcome the known limitations in the existing approaches, which could determine the structure changed from the one by X-ray in binding to a ligand or a partner protein to improve the modelled complex structure, for example. Protein structure change caused by interaction with other molecules is primarily important in discussing protein functional regulation. The structural change is not limited in the region around the binding site. Sometimes, it also causes rather global change including domain
Downregulation of the upstream binding factor1 by glycogen synthase kinase3β in myeloid cells induced to differentiate

The upstream binding factor 1 (UBF1), one of the proteins that regulate the activity of RNA polymerase I, is downregulated in 32D myeloid cells induced to differentiate into granulocytes, either by the type 1 insulin‐like growth factor (IGF‐1) or the granulocytic colony stimulating factor (G‐CSF). Downregulation of UBF1 is largely due to protein degradation, while mRNA levels are not affected. Inhibition of UBF1 degradation by lithium chloride (LiCl)and lactacystin suggest a role of glycogen synthase kinase β (GSK3β) in a proteasome‐dependent degradation of UBF. GSK3β phosphorylates in vitro and in vivo the UBF protein, which has five putative motifs for phosphorylation by GSK3β. Elimination and/or mutations of these motifs stabilize the UBF1 protein even in cells induced to differentiate. Conversely, a stably transfected, constitutively active GSK3β accelerates the downregulation of UBF1. We show further that activation of the differentiating protein C/EPBα in 32D cells transformed by the oncogenic BCR/ABL protein causes downregulation of UBF1. Finally, inhibition of differentiation of myeloid cells by a dominant negative mutant of Stat3 stabilizes the UBF1 protein, while rapamycin‐induced differentiation of myeloid cells downregulates UBF1 levels. Taken together, our results indicate that the induction of granulocytic differentiation in 32D murine myeloid cells causes the degradation of UBF1, via GSK3β and the proteasome pathway. J. Cell. Biochem. 100: 1154–1169, 2007. © 2006 Wiley‐Liss, Inc.
Importance of miR-20a expression in prostate cancer tissue.

BACKGROUND MicroRNAs (miRNAs), which are endogenously expressed regulatory noncoding RNAs, have an altered expression in tumor tissues. MiRNAs regulate cancer-related processes such as cell growth and tissue differentiation, and therefore, might function as oncogenes or tumor-suppressor genes. The aim of our study was to assess the expression of mir-20a, let-7a, miR-15a and miR-16 in prostate cancer (PCa) and benign prostatic hyperplasia (BPH) tissue and to investigate the relation between the expression of miRNAs and the clinicopathological features of PCa. PATIENTS AND METHODS The study group comprised 138 patients: 85 patients with BPH and 53 patients with PCa. The total RNA was isolated from the tissue specimen core and miRNA expressions were quantified using a real-time RT-PCR method (TaqMan MicroRNA Assays). U6snRNA was used for the normalization of the miRNA expression. RESULTS miR-20a expression was significantly higher in the group of patients with a Gleason score of 7-10 in comparison with the group of patients with a Gleason score of 0-6 (p=0.0082). We found no statistical differences in the miRNA expressions (mir-20a, let-7a, miR-15a and miR-16) in the PCa tissue samples in comparison with the BPH tissue samples. CONCLUSION Our result shows that the more dedifferentiated PCa cells have a higher expression of miR-20a and this supports the oncogenic role of miR-20a in PCa carcinogenesis. The evaluation of miRNA expression could yield new information about PCa pathogenesis.
Discovery of a human peptide sequence signaling islet neogenesis.

OBJECTIVE To identify triggers for islet neogenesis in humans that may lead to new treatments that address the underlying mechanism of disease for patients with type 1 or type 2 diabetes. METHODS In an effort to identify bioactive human peptide sequences that might trigger islet neogenesis, we evaluated amino acid sequences within a variety of mammalian pancreas-specific REG genes. We evaluated GenBank, the Basic Local Alignment Search Tool algorithm, and all available proteomic databases and developed large-scale protein-to-protein interaction maps. Studies of peptides of interest were conducted in human pancreatic ductal tissue, followed by investigations in mice with streptozocin-induced diabetes. RESULTS Our team has defined a 14-amino acid bioactive peptide encoded by a portion of the human REG3a gene we termed Human proIslet Peptide (HIP), which is well conserved among many mammals. Treatment of human pancreatic ductal tissue with HIP stimulated the production of insulin. In diabetic mice, administration of HIP improved glycemic control and significantly increased islet number. Bioinformatics analysis, coupled with biochemical interaction studies in a human pancreatic cell line, identified the human exostoses-like protein 3 (EXTL3) as a HIP-binding protein. HIP enhanced EXTL3 translocation from the membrane to the nucleus, in support of a model whereby EXTL3 mediates HIP signaling for islet neogenesis. CONCLUSION Our data suggest that HIP may be a potential stimulus for islet neogenesis and that the differentiation of new islets is a process distinct from beta cell proliferation within existing islets. Human clinical trials are soon to commence to determine the effect of HIP on generating new islets from one's own pancreatic progenitor cells.
Clinical investigation of cognitive styles in patients with acquired brain damage

This study aims to investigate relationships between the preference in use of visual–verbal cognitive representation and strategies and lesion site in patients with acquired brain injury. The Visualiser-Verbaliser Questionnaire (VVQ) and the Questionnaire on Visual and Verbal Strategies (QSVV) were administered to 48 patients by an examiner in an ambulatory setting. Data showed that the preference for verbalisation decreased in patients with a parietal focal lesion, who tended to use a mixed cognitive style. Patients with subcortical bilateral lesions verbalised more than patients with no lesion or right focal lesions. In general, damage in a specific area associated to a type of cognitive strategy may compromise its use, but does not lead to its extinction. From a neurorehabilitation perspective, findings suggest that patients can learn to use cognitive strategies to compensate for their deficits.
Assessments of pain in children and adolescents with cerebral palsy: a retrospective population‐based registry study

To explore pain screening in CPUP, a follow‐up surveillance programme for people with cerebral palsy (CP), specifically to describe reported pain prevalence, localizations, patterns of distribution; to compare with studies using psychometrically sound assessment instruments; and to assess agreement between pain documented in CPUP and medical records.
Lumbar Nerve Root Palsy After Adult Spinal Deformity Surgery

Study Design. A retrospective study was conducted to investigate the incidence and prognosis of postoperative lumbar nerve root palsy after surgical treatment for adult spinal deformity. Objective. To decipher the incidence of postoperative lumbar nerve root palsy and recovery in 361 adult spinal deformity patients who underwent 407 spinal fusion surgeries. Summary of Background Data. Although lumbar nerve root palsy is a known complication of spinal surgery, there are no large studies that have examined its incidence or prognosis. Methods. Three hundred and sixty-one consecutive patients who underwent 407 procedures for adult deformity spinal surgery were reviewed. Patients in this study did not have spinal cord injury or nerve root compression on the postoperative imaging study (obtained for change in neurologic examination). The incidence of nerve root palsy was based on postoperative muscle strength, which was followed for a minimum of 3 and an average of 7 years. Results. The overall incidence of lumbar nerve root palsy was 2.9% with a 1.4% incidence in primary and 3.8% incidence in revision surgery. The incidence was 0.9, 1.5, and 7.4% for fusion of <5 levels, 5 to 10 levels, and >10 levels, respectively. The incidence of nerve root palsy for posterior only, same day anterior-posterior, and staged posterior was 1.3, 3, and 7.2%, respectively. While L5 was the most commonly injured nerve root, all other lumbar nerve roots were also involved. There were no S1 injuries. Although there was some recovery in most injuries, Grade IV injuries had the best recovery at 1-year follow-up. Conclusion. Patients with increasingly complex spinal deformities are at a higher risk for postoperative lumbar nerve root palsy. These injuries can be treated nonoperatively when there is no identifiable cause on postoperative imaging studies.
Visual Hemispheric Asymmetry and Right-Left Confusion

From 357 university students two groups of 8 women each were selected, one group with high right-left confusion and the other without such confusion according to self-reports. Reaction times to stimuli tachistoscopically presented in visual hemifields were recorded to estimate the relationship between perceptual asymmetry and right-left confusion. A significant difference between hemifields and an interaction of hemifield by group appeared, whereas asymmetry in the highly confused group was not so related. According to a model of cerebral functioning in the formation of the body image, these results suggest subjects with high right-left confusion have greater hemispheric bilateralization.
Expression of COX-2, Ki-67, Cyclin D1, and P21 in Endometrial Endometrioid Carcinomas

COX-2, the isoform of cyclooxygenase inducible by cytokines, mitogens, and growth factors, appears to play an important role in inflammation and carcinogenesis. In the colon, COX-2 overexpression results in cell cycle alterations, and NSAIDs have proven effective in cancer chemoprevention. HNPCC (hereditary nonpolyposis colon cancer) is a clinically defined cancer susceptibility syndrome in which women are also at significantly increased risk for the development of endometrial carcinoma. The purpose of this study was to evaluate expression of COX-2 in benign and malignant endometrium in the context of other cell cycle and proliferation markers, including Ki-67, cyclin D1, and the cyclin-dependent kinase inhibitor, p21. Immunostains with COX-2, Ki-67, cyclin D1, and p21 antibodies were performed on formalin-fixed and paraffin-embedded tissue sections from 40 cases: 10 benign (5 atrophic and 5 proliferative) endometria, 6 hyperplasias (complex without atypia), and 24 endometrioid carcinomas (9 well, 4 moderately, and 11 poorly differentiated). Ki-67 was positive in all proliferative and neoplastic endometria. Cyclin D1 and p21 were both overexpressed in endometrial hyperplasia and endometrioid carcinomas. COX-2 was negative in the nonneoplastic endometrium, stained minimally in the well-differentiated endometrioid carcinomas, and stained most strongly in the moderately and poorly differentiated endometrioid carcinomas. Because cyclin D1 may function as an oncogene, its effects may dominate the usual inhibitory effect of a rising p21. Alternatively, it has been shown that p21 can promote cell cycle function by stabilizing cell cycle complexes. The overexpression of COX-2 in poorly differentiated endometrioid carcinoma and lack of expression in hyperplasia and well-differentiated carcinoma suggests that in this form of cancer, COX-2 may play a role in tumor progression rather than tumor initiation.
No need for routine closed suction drainage in elective arthroplasty of the hipA prospective randomized trial in 104 operations

BACKGROUND The purpose of this study was to determine the utility of closed suction drainage (CSD) in elective total hip arthroplasty (THA). PATIENTS AND METHODS We randomized 104 elective, consecutive THAs to receive drainage (53) or no drainage (51). 60 arthroplasties were cemented and 44 hybrid. RESULTS In the drainage group, 2 hematomas and 2 superficial wound infections occurred; there were no wound complications in the undrained group (p = 0.04). Patients receiving drainage had a greater reduction in hematocrit (10.4 vs 7.4) (p = 0.03), and longer hospital stay (5.1 days vs 4.7) (p = 0.01). At the 3-month follow-up, we found no deep wound infections in either group. INTERPRETATION We no longer use CSD in elective, primary, routine THA.