Miracle-dz/UniFAR-FTUs huggingface dataset:
Genotypic identification of two groups within the species Bacteroides fragilis by ribotyping and by analysis of PCR-generated fragment patterns and insertion sequence content

Molecular typing allowed the separation of the species Bacteroides fragilis into two genotypically distinct groups. A unique set of 50 strains of B. fragilis carrying the chromosomal metallo-beta-lactamase gene cfiA was subjected to a comparative analysis with respect to sets of up to 250 randomly collected strains devoid of this gene. The two groups were found to be distinct on the basis of the following results: (i) ribotyping, after DNA digestion with AvaI, revealed a practically homogeneous DNA fragment pattern for the cfiA-positive strains and distinct multiple patterns for the cfiA-negative strains; (ii) PCR, arbitrarily primed with an experimentally selected decamer, generated fragment patterns typical for the strains of each group; (iii) the three insertion sequences described to date in the species B. fragilis, i.e., IS4351, IS942, and IS1186, were all but confined to the cfiA-positive group, in which they were capable of providing promoter sequences for the transcription of cfiA; and (iv) the cepA gene, encoding the so-called endogenous cephalosporinase of B. fragilis, was found exclusively in the cfiA-negative group, in which it was present in ca. 70% of the strains. The cfiA-, cepA-negative fraction was not characterized further. In a natural population of 500 randomly selected strains of B. fragilis, the cfiA-positive and cfiA-negative groups represented ca. 3 and 97% of the strains, respectively. Analysis of 82 metabolic traits revealed no difference between the two groups.
The Development of an Immunohistochemical Method to Detect the Autophagy-Associated Protein LC3-II in Human Tumor Xenografts

Autophagy is believed to be an important process during tumorgenesis, and in recent years it has been shown to be modulated in response to a number of conventional anticancer agents. Furthermore, the development of targeted small molecule inhibitors, such as those to the PI3K-AKT-mTOR pathway, has presented a molecular link between the disruption of this signalling cascade and the process of autophagy. The cellular consequence of stimulating or inhibiting autophagy in cancer cells is not completely understood, so it is important that this process be monitored, along with antiproliferative and apoptotic biomarkers, in the preclinical setting. The field of autophagy is still evolving, and there is a constantly changing set of criteria for the assessment of the process in cells, tissues, and organs. The gold standard technique for analyzing autophagy in mammalian cells remains transmission electron microscopy, which has many limitations and is often difficult to perform on in vivo tissue including human tumor xenografts. In order to monitor autophagy in human tumor xenogaft tissue, we have taken the approach to develop an immunohistochemical (IHC) method for the detection of the autophagosome-associated protein, microtubule-associated protein 1 light chain 3 (LC3), in human tumor xenografts. After synthesis, LC3 is cleaved to form LC3-I, and upon induction of autophagy, LC3-I is conjugated to the lipid phosphatidylethanolamine to form LC3-II, which is tightly bound to the membrane of the autophagosome. It is thought that detection of endogenous LC3-II by IHC could be difficult because of the relatively low level of expression of the protein. Here we present the validation of an IHC method to detect LC3 in human tumor xenografts that we believe is able to distinguish LC3-I from LC3-II. It is hoped that this assay can become a useful tool for the detection of autophagy in preclinical xenograft models and determine the effects of anticancer therapies on the autophagic process.
Lower Extremity Trauma: Trends in the Management of Soft-Tissue Reconstruction of Open Tibia-Fibula Fractures

Background: Open lower leg fractures with exposed bone or tendon continue to be challenging for plastic surgeons. Microvascular free-tissue transfer increases the ability to close wounds, transfer vascularized bone, and prevent amputation, yet remains a complex, invasive procedure with significant complication rates, donor-site morbidity, and failure rates. This review documents the changing treatment protocol in the authors' institution for these injuries. Methods: Two hundred ninety consecutive open tibia-fibula fractures over a 12-year period (1992 to 2003) were retrospectively reviewed and methods and outcomes were compared by grouping the fractures into 4-year intervals. Results: The number of open lower extremity fractures increased, whereas the distribution of Gustilo grade I to III fractures remained unchanged. Overall, free-tissue transfer was performed less frequently and constituted 20 percent of reconstructions in period 1 (1992 to 1995), 11 percent in period 2 (1996 to 1999), and 5 percent in period 3 (2000 to 2003). For the most severe fractures, Gustilo grade III, free-flap reconstruction has decreased significantly, constituting 42 percent, 26 percent, and 11 percent of procedures in periods 1, 2, and 3, respectively. Local flaps for grade III fractures have remained relatively constant throughout the study. In contrast, local wound care for grade III fractures, including skin grafts, delayed primary closures, and secondary intention closures has significantly increased from 22 percent to 49 percent of reconstructions from periods 1 through 3. In 1997, the authors began to use the vacuum-assisted closure device and now use it in nearly half of all open fractures. Despite this trend, there has been no change in infection, amputation, or malunion/nonunion rates and a decrease in reoperation rate with at least 1-year follow-up. Conclusions: These results demonstrate a change in practice, with a trend down the reconstructive ladder, currently using fewer free flaps and more delayed closures and skin grafts with frequent use of the vacuum-assisted closure sponge. Possible reasons for this change are a better understanding of lower leg vascular anatomy and better use of improved wound care technology.
The relationship between depression and regional cerebral blood flow in Parkinson’s disease and the effect of selegiline treatment

Imamura K, Okayasu N, Nagatsu T. The relationship between depression and regional cerebral blood flow in Parkinson’s disease and the effect of selegiline treatment. Acta Neurol Scand: 2011: 124: 28–39. © 2010 John Wiley & Sons A/S.
Canonical Transient Receptor Potential 1 Plays a Role in Basic Fibroblast Growth Factor (bFGF)/FGF Receptor-1-Induced Ca2+ Entry and Embryonic Rat Neural Stem Cell Proliferation

Basic fibroblast growth factor (bFGF) and its major receptor FGF receptor-1 (FGFR-1) play an important role in the development of the cortex. The mechanisms underlying the mitogenic role of bFGF/FGFR-1 signaling have not been elucidated. Intracellular Ca2+ concentrations ([Ca2+]i) in proliferating cortical neuroepithelial cells are markedly dependent on Ca2+ entry (Maric et al., 2000a). The absence of voltage-dependent Ca2+ entry channels, which emerge later, indicates that other membrane mechanisms regulate [Ca2+]i during proliferation. Canonical transient receptor potential (TRPC) family channels are candidates because they are voltage independent and are expressed during CNS development (Strübing et al., 2003). Here, we investigated the involvement of TRPC1 in bFGF-mediated Ca2+ entry and proliferation of embryonic rat neural stem cells (NSCs). Both TRPC1 and FGFR-1 are expressed in the embryonic rat telencephalon and coimmunoprecipitate. Quantitative fluorescence-activated cell sorting analyses of phenotyped telencephalic dissociates show that ∼80% of NSCs are TRPC1+, proliferating, and express FGFR-1. Like NSCs profiled ex vivo, NSC-derived progeny proliferating in vitro coexpress TRPC1 and FGFR1. Antisense knock-down of TRPC1 significantly decreases bFGF-mediated proliferation of NSC progeny, reduces the Ca2+ entry component of the Cai2+ response to bFGF without affecting Ca2+ release from intracellular stores or 1-oleoyl-2-acetyl-sn-glycerol-induced Ca2+ entry, and significantly blocks an inward cation current evoked by bFGF in proliferating NSCs. Both Ca2+ influx evoked by bFGF and NSC proliferation are attenuated by Gd3+ and SKF96365, two antagonists of agonist-stimulated Ca2+ entry. Together, these results show that TRPC1 contributes to bFGF/FGFR-1-induced Ca2+ influx, which is involved in self-renewal of embryonic rat NSCs.
Photovoltaics in Van der Waals Heterostructures

The peculiar nature of light-matter interaction in atomically thin transition metal dichalcogenides is recently under examination for application in novel optoelectronic devices. Here, we show that heterostructures composed of two or more such layers can be used for solar energy harvesting. The strong absorption in these atomically thin layers makes it possible to achieve an efficient power conversion with a minimal amount of active material. We describe in detail two different fabrication techniques that allow to realize heterostructures with clean, atomically sharp interfaces. The observed electrical and photovoltaic properties are analyzed. Our findings suggest that, accompanied by the advances in large area fabrication of atomically thin transition metal dichalcogenides, van der Waals heterostructures are promising candidates for a new generation of excitonic solar cells.
Full Virulence of Pseudomonas aeruginosa Requires OprF

ABSTRACT OprF is a general outer membrane porin of Pseudomonas aeruginosa, a well-known human opportunistic pathogen associated with severe hospital-acquired sepsis and chronic lung infections of cystic fibrosis patients. A multiphenotypic approach, based on the comparative study of a wild-type strain of P. aeruginosa, its isogenic oprF mutant, and an oprF-complemented strain, showed that OprF is required for P. aeruginosa virulence. The absence of OprF results in impaired adhesion to animal cells, secretion of ExoT and ExoS toxins through the type III secretion system (T3SS), and production of the quorum-sensing-dependent virulence factors pyocyanin, elastase, lectin PA-1L, and exotoxin A. Accordingly, in the oprF mutant, production of the signal molecules N-(3-oxododecanoyl)-l-homoserine lactone and N-butanoyl-l-homoserine lactone was found to be reduced and delayed, respectively. Pseudomonas quinolone signal (PQS) production was decreased, while its precursor, 4-hydroxy-2-heptylquinoline (HHQ), accumulated in the cells. Taken together, these results show the involvement of OprF in P. aeruginosa virulence, at least partly through modulation of the quorum-sensing network. This is the first study showing a link between OprF, PQS synthesis, T3SS, and virulence factor production, providing novel insights into virulence expression.
N-acetylcysteine effectively mitigates cadmium-induced oxidative damage and cell death in Leydig cells in vitro

Abstract Context: Cadmium (Cd) is known to cause severe damage to various organs including lung, liver, kidney, brain and reproductive system. Several studies have reported the induction of oxidative stress pathways following Cd exposure. Objective: Since oxidative stress is also deemed responsible for inducing male infertility, a growing worldwide concern, we tried to understand whether the antioxidant N-acetylcysteine (NAC) can be a potential therapeutic agent to counter Cd toxicity using primary Leydig cells. Materials and methods: This study highlights the initial cellular alterations which culminate in cell death induction. Primary Leydig cells were isolated from 28-day-old male Wistar rats, exposed to various concentrations of Cd in vitro and biochemical and cell death parameters were evaluated to understand the effect of Cd. NAC pre-treatment was done to understand its protective efficacy. Results: Following Cd exposure to Leydig cells in vitro, we found simultaneous intracellular calcium (Ca2+) increase and reduction in mitochondrial membrane polarization at 30 min, followed by significant induction of reactive oxygen species and MAPK–extracellular-regulated kinases with concurrent glutathione depletion at 1 h, and significant cell death (both necrotic and apoptotic) at 6 and 18 h, respectively. Pre-treatment with NAC abrogated all these toxic manifestations and showed significantly reduced cell death. NAC also rescued the expression of 3-βHSD, a major steroidogenic protein. Discussion and conclusion: Taken together, these data illustrated that NAC can be used as a potential protective agent against Cd-induced testicular toxicity, especially with regards to oxidative stress-induced Leydig cell toxicity.
Electrophysiological alternans and restitution during acute regional ischaemia in myocardium of anaesthetized pig.

1. Alternate long and short action potential durations, or electrical alternans, has only been sporadically observed in ischaemic myocardium in situ. We systematically studied alternans in the latter to characterize the phenomenon, relate it to ventricular arrhythmia and suggest possible mechanisms. 2. Sixteen Landrace pigs were anaesthetized (Azaperone, N2O and O2), ventilated and the hearts exposed. A branch of the left coronary artery was ligated. Left intraventricular and systemic pressures were monitored. Monophasic action potentials were recorded simultaneously with up to five suction electrodes in and around the proposed ischaemia area. 3. A computer measured the duration of every action potential, at several phases of repolarization, throughout the first hour of ischaemia. This allowed the systematic study of the alternans. Measurements during defined stimulus protocols were also made for the construction of electrical restitution curves. 4. Alternans was found in all recordings within the ischaemic area and in two‐thirds of those in the ‘border’ area. There was no alternans in non‐ischaemic areas. 5. The alternans, when action potential duration was plotted for every beat, appeared as an oscillation which was pleomorphic. It could be: (a) stable for hundreds of beats; (b) switched or triggered (by one extraneous beat having a different cycle length) between one stable state with high and one with low or absent alternans; (c) damped; (d) undamped to take a crescendo form, sometimes preceding ventricular fibrillation. 6. The alternans in general showed an ill‐defined peak incidence between about 200 to 1500 beats after the onset of ischaemia, and a clearer late peak at about 3000 beats. These periods occurred at about 2‐7 min and 15‐40 min, corresponding to so‐called phase 1A and 1B arrhythmia respectively. Only the late peak was seen with triggered alternans. 7. The electrical restitution curve for the action potential duration during ischaemia when compared with curves, constructed with data from non‐ischaemic myocardium, showed a progressive depression in plateau, a reduction in magnitude and was flattened at 1 h. However, there was a reversal or reduction in decline at about 15‐45 min. 8. We propose that electrical alternans is a distinctive electrophysiological characteristic of ischaemic myocardium which may be causally related to ventricular arrhythmia and fibrillation, and that at least two mechanisms contribute to the alternans: (i) electrical restitution of the action potential and (ii) changes in intracellular calcium cycling.
EBM, HTA, and CER: clearing the confusion.

CONTEXT The terms evidence-based medicine (EBM), health technology assessment (HTA), comparative effectiveness research (CER), and other related terms lack clarity and so could lead to miscommunication, confusion, and poor decision making. The objective of this article is to clarify their definitions and the relationships among key terms and concepts. METHODS This article used the relevant methods and policy literature as well as the websites of organizations engaged in evidence-based activities to develop a framework to explain the relationships among the terms EBM, HTA, and CER. FINDINGS This article proposes an organizing framework and presents a graphic demonstrating the differences and relationships among these terms and concepts. CONCLUSIONS More specific terminology and concepts are necessary for an informed and clear public policy debate. They are even more important to inform decision making at all levels and to engender more accountability by the organizations and individuals responsible for these decisions.
The 2016 European Thyroid Association/European Group on Graves' Orbitopathy Guidelines for the Management of Graves' Orbitopathy

Graves' orbitopathy (GO) is the main extrathyroidal manifestation of Graves' disease, though severe forms are rare. Management of GO is often suboptimal, largely because available treatments do not target pathogenic mechanisms of the disease. Treatment should rely on a thorough assessment of the activity and severity of GO and its impact on the patient's quality of life. Local measures (artificial tears, ointments and dark glasses) and control of risk factors for progression (smoking and thyroid dysfunction) are recommended for all patients. In mild GO, a watchful strategy is usually sufficient, but a 6-month course of selenium supplementation is effective in improving mild manifestations and preventing progression to more severe forms. High-dose glucocorticoids (GCs), preferably via the intravenous route, are the first line of treatment for moderate-to-severe and active GO. The optimal cumulative dose appears to be 4.5-5 g of methylprednisolone, but higher doses (up to 8 g) can be used for more severe forms. Shared decision-making is recommended for selecting second-line treatments, including a second course of intravenous GCs, oral GCs combined with orbital radiotherapy or cyclosporine, rituximab or watchful waiting. Rehabilitative treatment (orbital decompression surgery, squint surgery or eyelid surgery) is needed in the majority of patients when GO has been conservatively managed and inactivated by immunosuppressive treatment.
Partial discharge resistant characteristics of epoxy nanocomposites

Epoxy nanocomposite samples with a good dispersion of alumina nanoparticles in epoxy matrix were prepared and experiments were performed to measure their partial discharge resistant characteristics. Epoxy alumina nanocomposites with 0.1, 1, 5, 10 and 15 wt% nanofillers were prepared in the laboratory and partial discharge (PD) experiments were conducted at a voltage of 10 kV for different durations using IEC (b) type electrodes. The degradation of the sample surfaces were analyzed using SEM techniques, surface profile studies, FTIR spectroscopy as well as PD studies. An attempt was made to understand the interaction dynamics between the nanoparticle and the epoxy chain by measuring the glass transition temperature of the nanocomposites. The partial discharge resistance obtained for the nanocomposites are compared with those of unfilled epoxy and epoxy microcomposites. It was observed that even with 0.1 wt% of nanofiller added to the epoxy matrix, the partial discharge resistance to degradation gets improved considerably. It was also observed that the inter particle distance has a significant effect on the discharge resistance to degradation. The improvement in the degradation resistance is attributed to the interactions between the nanoparticle and the epoxy chain. A possible mechanism for the surface degradation of nanocomposites has been proposed.
Residual oil fly ash exposure enhances allergic sensitization to house dust mite.

Epidemiological studies have shown an association between elevated levels of particulate matter air pollution and increased morbidity and hospital visits in asthmatics. Residual oil fly ash (ROFA) is a primary combustion particle containing sulfate and metals such as vanadium, nickel, and iron. In this study the effect of ROFA on sensitization to house dust mite (HDM) was examined in a Brown Norway rat model of pulmonary allergy. Rats were instilled via the trachea with 200 or 1000 micrograms ROFA 3 days prior to local sensitization with 10 micrograms HDM and were challenged with 10 micrograms HDM 14 days later. Immunological endpoints were examined at 2, 7, and 14 days after sensitization and at 2 and 7 days after challenge (16 and 21 days post-sensitization, respectively). Antigen-specific immunoglobulin E and associated immediate bronchoconstriction responses to antigen challenge were increased in the ROFA-treated groups compared with the HDM control group. Lymphocyte proliferation to antigen was enhanced at Days 7 and 21 in the bronchial lymphocytes of ROFA-treated groups. Bronchoalveolar lavage fluid (BALF) eosinophil numbers and lactate dehydrogenase were significantly increased in the 1000 micrograms ROFA group at Days 2 and 16, BALF total proteins were elevated at Days 2 and 7 in both ROFA-treated groups, and BALF interleukin (IL)-10 was elevated in the 1000 micrograms ROFA group at Day 2. These results suggest that ROFA has an adjuvant effect on sensitization to HDM.
HTAPP: High‐throughput autonomous proteomic pipeline

Recent advances in the speed and sensitivity of mass spectrometers and in analytical methods, the exponential acceleration of computer processing speeds, and the availability of genomic databases from an array of species and protein information databases have led to a deluge of proteomic data. The development of a lab‐based automated proteomic software platform for the automated collection, processing, storage, and visualization of expansive proteomic data sets is critically important. The high‐throughput autonomous proteomic pipeline described here is designed from the ground up to provide critically important flexibility for diverse proteomic workflows and to streamline the total analysis of a complex proteomic sample. This tool is composed of a software that controls the acquisition of mass spectral data along with automation of post‐acquisition tasks such as peptide quantification, clustered MS/MS spectral database searching, statistical validation, and data exploration within a user‐configurable lab‐based relational database. The software design of high‐throughput autonomous proteomic pipeline focuses on accommodating diverse workflows and providing missing software functionality to a wide range of proteomic researchers to accelerate the extraction of biological meaning from immense proteomic data sets. Although individual software modules in our integrated technology platform may have some similarities to existing tools, the true novelty of the approach described here is in the synergistic and flexible combination of these tools to provide an integrated and efficient analysis of proteomic samples.