Miracle-dz/UniFAR-FTUs huggingface dataset:
Skeletal complications of brucellosis: A study of 464 cases in Babol, Iran

Background: Skeletal complication of brucellosis is common in endemic region of brucellosis, but its frequency has not been clearly determined. The aim of this study was to determine the frequency of skeletal complication in brucellosis patients in Babol, north of Iran. Methods: From 2005-2015, 1252 cases of brucellosis were diagnosed at the Department of Infectious Diseases, Ayatollah Rouhani Teaching Hospital, in Babol, North of Iran. The diagnosis of brucellosis was established using serum agglutination test (SAT≥1/160), and 2-mercaptoethanol (2ME≥ 1/80) with clinical and epidemiological findings compatible with brucellosis. Among them, 464 (37.1%) cases demonstrated skeletal complication. The diagnosis of skeletal involvement was established with appropriate diagnostic facilities. The data were collected and analyzed. Results: The mean age of these patients (299 males, 165 females) was 33.2±17.6 years. Three hundred-thirty four (72%) cases were from rural areas. In 350 (75.4%) patients with peripheral arthritis, 242 (52.1%) cases were monoarthritis. Furthermore the knee arthritis was seen in 148 (31.9%) patients and hip in 54 (11.6) cases. Sacroiliitis was seen in 59 (12.7%) patients and spondylitis in 55 (11.9%) cases. There were no significant differences regarding the occurrence of these focal lesions in both sexes. Conclusion: The results show that about one-third of brucellosis in human is associated with skeletal complication. Peripheral arthritis, sacroiliitis and spondylitis are the frequent skeletal complications of human brucellosis.
Woodpecker: An Automatic Methodology for Machine Translation Diagnosis with Rich Linguistic Knowledge

Different from the ＂black-box＂ evaluation, the diagnostic evaluation aims to provide a better explanatory power into various aspects of the performance of artificial intelligence systems. However, for machine translation (MT) systems, due to its complexity and knowledge dependency, such diagnostic evaluation often demands a large amount of manual work. To tackle this problem, we propose an automatic diagnostic evaluation methodology, called Woodpecker, which enables multi-factored evaluation of MT systems based on linguistic categories and automatically constructed linguistic checkpoints. The taxonomy of the categories is defined with rich linguistic knowledge, including phenomena on different linguistic levels. The instances of the categories are composed into test cases called linguistic checkpoints. We present a method that automatically extracts checkpoints from parallel sentences, through which, Woodpecker can automatically monitor a MT system in translating various linguistic phenomena, thereby facilitating diagnostic evaluation. The effectiveness of Woodpecker is verified through in-house experiments and open MT evaluation tracks on various types of MT systems.
Portholes: supporting awareness in a distributed work group

We are investigating ways in which media space technologies can support distributed work groups through access to information that supports general awareness. Awareness involves knowing who is “around”, what activities are occurring, who is talking with whom; it provides a view of one another in the daily work environments. Awareness may lead to informal interactions, spontaneous connections, and the development of shared cultures—all important aspects of maintaining working relationships which are denied to groups distributed across multiple sites. The Portholes project, at Rank Xerox EuroPARC in Cambridge, England, and Xerox PARC in Palo Alto, California, demonstrates that awareness can be supported across distance. A data network provides a shared database of image information that is regularly updated and available at all sites. Initial experiences of the system in use at EuroPARC and PARC suggest that Portholes both supports shared awareness and helps to build a “sense of community”.
Highly conserved type 1 pili promote enterotoxigenic E. coli pathogen-host interactions

Enterotoxigenic Escherichia coli (ETEC), defined by their elaboration of heat-labile (LT) and/or heat-stable (ST) enterotoxins, are a common cause of diarrheal illness in developing countries. Efficient delivery of these toxins requires ETEC to engage target host enterocytes. This engagement is accomplished using a variety of pathovar-specific and conserved E. coli adhesin molecules as well as plasmid encoded colonization factors. Some of these adhesins undergo significant transcriptional modulation as ETEC encounter intestinal epithelia, perhaps suggesting that they cooperatively facilitate interaction with the host. Among genes significantly upregulated on cell contact are those encoding type 1 pili. We therefore investigated the role played by these pili in facilitating ETEC adhesion, and toxin delivery to model intestinal epithelia. We demonstrate that type 1 pili, encoded in the E. coli core genome, play an essential role in ETEC virulence, acting in concert with plasmid-encoded pathovar specific colonization factor (CF) fimbriae to promote optimal bacterial adhesion to cultured intestinal epithelium (CIE) and to epithelial monolayers differentiated from human small intestinal stem cells. Type 1 pili are tipped with the FimH adhesin which recognizes mannose with stereochemical specificity. Thus, enhanced production of highly mannosylated proteins on intestinal epithelia promoted FimH-mediated ETEC adhesion, while conversely, interruption of FimH lectin-epithelial interactions with soluble mannose, anti-FimH antibodies or mutagenesis of fimH effectively blocked ETEC adhesion. Moreover, fimH mutants were significantly impaired in delivery of both heat-stable and heat-labile toxins to the target epithelial cells in vitro, and these mutants were substantially less virulent in rabbit ileal loop assays, a classical model of ETEC pathogenesis. Collectively, our data suggest that these highly conserved pili play an essential role in virulence of these diverse pathogens.
Do structured arrangements for multidisciplinary peer group supervision make a difference for allied health professional outcomes?

Peer group supervision, particularly in multidisciplinary formats, presents a potential means of providing professional support, and specifically clinical supervision, for allied health professionals. Debate exists regarding the extent to which the activities of these groups should be formalized. Results drawn from an evaluation of a large-scale peer group supervision initiative are described. Analysis of 192 responses from professionals involved in peer groups indicates that participants in groups that used formal documentation – which adopted the tools provided in training, and particularly those that used formal evaluation of their groups – rated their groups as having better processes and greater impact. Interestingly, multidisciplinary peer groups were rated as having similar impacts, processes, and purposes as the more homogenous single-discipline groups. It is concluded that the implementation of formal arrangements enhances the processes and outcomes of peer groups implemented for professional support and clinical supervision. Multidisciplinary membership of such groups is perceived as equally beneficial as single-discipline groups.
11C-Dihydrotetrabenazine PET of the Pancreas in Subjects with Long-Standing Type 1 Diabetes and in Healthy Controls

Type 2 vesicular monoamine transporter (VMAT2), found in the brain, is also expressed by β-cells of the pancreas in association with insulin. Preclinical experiments suggested that 11C-dihydrotetrabenazine PET–measured VMAT2 binding might serve as a biomarker of β-cell mass. We evaluated the feasibility of 11C-dihydrotetrabenazine PET quantification of pancreatic VMAT2 binding in healthy subjects and patients with long-standing type 1 diabetes. Methods: 11C-Dihydrotetrabenazine PET was performed on 6 patients and 9 controls. VMAT2 binding potential (BPND) was estimated voxelwise by using the renal cortex as reference tissue. As an index of total pancreatic VMAT2, the functional binding capacity (the sum of voxel BPND × voxel volume) was calculated. Pancreatic BPND, functional binding capacity, and stimulated insulin secretion measurements were compared between groups. Results: The pancreatic mean BPND was decreased in patients (1.86 ± 0.05) to 86% of control values (2.14 ± 0.08) (P = 0.01). In controls, but not in patients, BPND correlated with stimulated insulin secretion (r2 = 0.50, P = 0.03). The average functional binding capacity was decreased by at least 40% in patients (P = 0.001). The changes in functional binding capacity and BPND were less than the near-complete loss of stimulated insulin secretion observed in patients (P = 0.001). Conclusion: These results suggest that 11C-dihydrotetrabenazine PET allows quantification of VMAT2 binding in the human pancreas. However, BPND and functional binding capacity appear to overestimate β-cell mass given the near-complete depletion of β-cell mass in long-standing type 1 diabetes, which may be due to higher nonspecific binding in the pancreas than in the renal cortex.
Neuronal expression of the transcription factor serum response factor modulates myelination in a mouse multiple sclerosis model

In multiple sclerosis (MS), neurons in addition to inflammatory cells are now considered to mediate disease origin and progression. So far, molecular and cellular mechanisms of neuronal MS contributions are poorly understood. Herein we analyzed whether neuron‐restricted signaling by the neuroprotective transcription factor serum response factor (SRF) modulates de‐ and remyelination in a rodent MS model. In the mouse cuprizone model, neuron‐ (Srf flox/flox;CaMKCreERT2) but not glia‐specific (Srf flox/flox;PlpCreERT2) SRF depletion impaired demyelination suggesting impaired debris clearance by astrocytes and microglia. This supports an important role of SRF expression in neurons but not oligodendrocytes in de‐ and remyelination. During remyelination, NG2‐ and OLIG2‐positive cells of the oligodendrocyte lineage as well as de novo mRNA synthesis of myelin genes were also reduced in neuron‐specific Srf mutants. Using the stripe assay, we demonstrate that cortices of cuprizone‐fed wild‐type mice elicited astrocyte and microglia activation whereas this was abrogated in cuprizone‐fed neuron‐specific Srf mutants. We identified CCL chemokines (e.g. CCL2) as neuron‐derived SRF‐regulated paracrine signals rescuing immune cell activation upon neuronal SRF deletion. In summary, we uncovered important roles of neurons and neuronally expressed SRF in MS associated de‐ and remyelination. GLIA 2015;63:958–976
Automatic chromosome pairing using mutual information

Cytogenetics is a key tool in the detection of acquired chromosomal abnormalities and in the diagnosis of genetic diseases such as leukemia. The karyotyping is a set of procedures, in the scope of the cytogenetics, that produces a visual representation of the 46 chromosomes (called karyogram), paired and arranged in decreasing order of size.
Sprouting, regeneration and circuit formation in the injured spinal cord: factors and activity

Central nervous system (CNS) injuries are particularly traumatic, owing to the limited capabilities of the mammalian CNS for repair. Nevertheless, functional recovery is observed in patients and experimental animals, but the degree of recovery is variable. We review the crucial characteristics of mammalian spinal cord function, tract development, injury and the current experimental therapeutic approaches for repair. Regenerative or compensatory growth of neurites and the formation of new, functional circuits require spontaneous and experimental reactivation of developmental mechanisms, suppression of the growth-inhibitory properties of the adult CNS tissue and specific targeted activation of new connections by rehabilitative training.
Properties of Rapeseed (Brassica napus) Stalks Fibers

For any type of pulping process, the chemical composition of raw materials is the determining factor of pulping yield, while fiber dimensions establish the pulp strength and dictate its final use. In this study, an attempt was made to present the chemical and morphological characteristics of Brassica napus stalk fibers. The chemical compositions of raw material and Kraft-delignified fibers were analyzed for the macromolecular substances content (cellulose, hemicelluloses, pentosans, and lignin) and low- molecular-weight components (extractives, soluble, inorganic). With regard to morphology features, such as fiber length, width, and wall thickness of pulp, samples were measured using digital microscope system and scanning electron microscope. It is concluded that the properties of rapeseed stalk fibers, which are commonly encountered in other nonwood and hardwood papermaking fibers, have the potential for being used for manufacturing different paper products.
Time and life perception in the terminally ill: its utility in screening for depression.

OBJECTIVE The objective was to explore the utility of a new three-item depression screening tool concerning time and life perception (TLP-3), compared with the DSM-IV criteria. METHODS This was a cross-sectional study of 63 Portuguese terminally ill patients, from May 2010 to November 2012. Patients were eligible if they fulfilled the following inclusion criteria: age ≥18 years old; having a life-threatening disease with prognosis of 6 months or less; no evidence of dementia or delirium, based on documentation within the medical chart or by clinical consensus; Mini Mental State score ≥20; being able to read and speak Portuguese; and provision of written informed consent. Participants were assessed for depression using DSM-IV criteria and the newly developed TLP-3. Screening performance for depression using the TLP-3 compared with DSM-IV was calculated using measures of sensitivity, specificity, positive and negative predictive values. Logistic regression was calculated with the aim of identifying variables with the best predictive ability for diagnosing depression. RESULTS After logistic regression analysis was made to all three items composing TLP-3, only two items were maintained (OR=2.9, 95% CI [0.9-8.7]; OR=7.6, 95% CI [0.9-65.3], respectively). This final regression model composed of two questions (TLP-2) was able to diagnose correctly 70% of the depressed patients with a sensitivity of 63% and a specificity of 74%. The area under the ROC curve was 72% (95% CI [59-85]). CONCLUSION TLP-3 is a novel and clinically applicable approach to assessing depression among palliative care patients. Further investigation is needed on the psychological significance of time and life perception distortions, and its possible application to screen for depression among patients nearing end of life.
Free Material Optimization with Fundamental Eigenfrequency Constraints

The goal of this paper is to formulate and solve free material optimization problems with constraints on the smallest eigenfrequency of the optimal structure. A natural formulation of this problem as a linear semidefinite program turns out to be numerically intractable. As an alternative, we propose a new approach, which is based on a nonlinear semidefinite low-rank approximation of the semidefinite dual. We introduce an algorithm based on this approach and analyze its convergence properties. The article is concluded by numerical experiments proving the effectiveness of the new approach.
Widening access to UK medical education for under-represented socioeconomic groups: modelling the impact of the UKCAT in the 2009 cohort

Objective To determine whether the use of the UK clinical aptitude test (UKCAT) in the medical schools admissions process reduces the relative disadvantage encountered by certain sociodemographic groups. Design Prospective cohort study. Setting Applicants to 22 UK medical schools in 2009 that were members of the consortium of institutions utilising the UKCAT as a component of their admissions process. Participants 8459 applicants (24 844 applications) to UKCAT consortium member medical schools where data were available on advanced qualifications and socioeconomic background. Main outcome measures The probability of an application resulting in an offer of a place on a medicine course according to seven educational and sociodemographic variables depending on how the UKCAT was used by the medical school (in borderline cases, as a factor in admissions, or as a threshold). Results On univariate analysis all educational and sociodemographic variables were significantly associated with the relative odds of an application being successful. The multilevel multiple logistic regression models, however, varied between medical schools according to the way that the UKCAT was used. For example, a candidate from a non-professional background was much less likely to receive a conditional offer of a place compared with an applicant from a higher social class when applying to an institution using the test only in borderline cases (odds ratio 0.51, 95% confidence interval 0.45 to 0.60). No such effect was observed for such candidates applying to medical schools using the threshold approach (1.27, 0.84 to 1.91). These differences were generally reflected in the interactions observed when the analysis was repeated, pooling the data. Notably, candidates from several under-represented groups applying to medical schools that used a threshold approach to the UKCAT were less disadvantaged than those applying to the other institutions in the consortium. These effects were partially reflected in significant differences in the absolute proportion of such candidates finally taking up places in the different types of medical schools; stronger use of the test score (as a factor or threshold) was associated with a significantly increased odds of entrants being male (1.74, 1.25 to 2.41) and from a low socioeconomic background (3.57, 1.03 to 12.39). There was a non-significant trend towards entrants being from a state (non-grammar) school (1.60, 0.97 to 2.62) where a stronger use of the test was employed. Use of the test only in borderline cases was associated with increased odds of entrants having relatively low academic attainment (5.19, 2.02 to 13.33) and English as a second language (2.15, 1.03 to 4.48). Conclusions The use of the UKCAT may lead to more equitable provision of offers to those applying to medical school from under-represented sociodemographic groups. This may translate into higher numbers of some, but not all, relatively disadvantaged students entering the UK medical profession.
Intra-Arterial Bone Marrow Mononuclear Cells in Ischemic Stroke: A Pilot Clinical Trial

Background and Purpose— Bone marrow mononuclear cell (BM-MNC) intra-arterial transplantation improves recovery in experimental models of ischemic stroke. We aimed to assess the safety, feasibility, and biological effects of autologous BM-MNC transplantation in patients with stroke. Methods— A single-blind (outcomes assessor) controlled Phase I/II trial was conducted in patients with middle cerebral artery stroke. Autologous BM-MNCs were injected intra-arterially between 5 and 9 days after stroke. Follow-up was done for up to 6 months and blood samples were collected for biological markers. The primary outcome was safety and feasibility of the procedure. The secondary outcome was improvement in neurological function. Results— Ten cases (BM-MNC-treated) and 10 control subjects (BM-MNC-nontreated) were consecutively included. Mean National Institutes of Health Stroke Scale before the procedure was 15.6. Mean BM-MNCs injected were 1.59×108. There was no death, stroke recurrence, or tumor formation during follow-up, although 2 cases had an isolate partial seizure at 3 months. After transplantation, higher plasma levels of beta nerve growth factor (&bgr;-nerve growth factor) were found compared with control subjects (P=0.02). There were no significant differences in neurological function at 180 days. A trend to positive correlation between number of CD34+ cells injected and Barthel Index was found (r=0.56, P=0.09). Conclusions— Intra-arterial BM-MNC transplantation in subacute ischemic stroke is feasible and seems to be safe. Larger randomized trials are needed to confirm the safety and elucidate the efficacy of BM-MNC transplantation. Clinical Trial Registration-URL— www.clinicaltrials. gov. Unique identifier: NCT00761982.
Identification and Screening of Introduced Tomato Varieties Resistant to late Blight

Tomato late blight disease that infected by Phytophthora infestans (Mont.) de Bary has already become one of the main obstacles that influence the tomato production. To resolve tomato late blight disease, cultivating the disease-resistant breed is importance. Based on the previous study, different introduced varieties were used as materials in this test for the identification and varieties selection of tomato resistant to late blight, by measuring the DIS of inoculated seedlings and detached leaves. It indicated that Jingle 502 and O-33-1 are possible to become resistant varieties to late blight or the parents for cultivating new disease resistant varieties.
Polyproline II structure in a sequence of seven alanine residues

A sequence of seven alanine residues—too short to form an α-helix and whose side chains do not interact with each other—is a particularly simple model for testing the common description of denatured proteins as structureless random coils. The 3JHNα coupling constants of individual alanine residues have been measured from 2 to 56°C by using isotopically labeled samples. The results display a thermal transition between different backbone conformations, which is confirmed by CD spectra. The NMR results suggest that polyproline II is the dominant conformation at 2°C and the content of β strand is increased by approximately 10% at 55°C relative to that at 2°C. The polyproline II conformation is consistent with recent studies of short alanine peptides, including structure prediction by ab initio quantum mechanics and solution structures for both a blocked alanine dipeptide and an alanine tripeptide. CD and other optical spectroscopies have found structure in longer “random coil” peptides and have implicated polyproline II, which is a major backbone conformation in residues within loop regions of protein structures. Our result suggests that the backbone conformational entropy in alanine peptides is considerably smaller than estimated by the random coil model. New thermodynamic data confirm this suggestion: the entropy loss on alanine helix formation is only 2.2 entropy units per residue.
A molecular switch that controls cell spreading and retraction

Integrin-dependent cell spreading and retraction are required for cell adhesion, migration, and proliferation, and thus are important in thrombosis, wound repair, immunity, and cancer development. It remains unknown how integrin outside-in signaling induces and controls these two opposite processes. This study reveals that calpain cleavage of integrin β3 at Tyr759 switches the functional outcome of integrin signaling from cell spreading to retraction. Expression of a calpain cleavage–resistant β3 mutant in Chinese hamster ovary cells causes defective clot retraction and RhoA-mediated retraction signaling but enhances cell spreading. Conversely, a calpain-cleaved form of β3 fails to mediate cell spreading, but inhibition of the RhoA signaling pathway corrects this defect. Importantly, the calpain-cleaved β3 fails to bind c-Src, which is required for integrin-induced cell spreading, and this requirement of β3-associated c-Src results from its inhibition of RhoA-dependent contractile signals. Thus, calpain cleavage of β3 at Tyr759 relieves c-Src–mediated RhoA inhibition, activating the RhoA pathway that confines cell spreading and causes cell retraction.