Miracle-dz/UniFAR-FTUs huggingface dataset:
EFA6, a sec7 domain‐containing exchange factor for ARF6, coordinates membrane recycling and actin cytoskeleton organization

We have identified a human cDNA encoding a novel protein, exchange factor for ARF6 (EFA6), which contains Sec7 and pleckstrin homology domains. EFA6 promotes efficient guanine nucleotide exchange on ARF6 and is distinct from the ARNO family of ARF1 exchange factors. The protein localizes to a dense matrix on the cytoplasmic face of plasma membrane invaginations, induced on its expression. We show that EFA6 regulates endosomal membrane recycling and promotes the redistribution of transferrin receptors to the cell surface. Furthermore, expression of EFA6 induces actin‐based membrane ruffles that are inhibited by co‐expression of dominant‐inhibitory mutant forms of ARF6 or Rac1. Our results demonstrate that by catalyzing nucleotide exchange on ARF6 at the plasma membrane and by regulating Rac1 activation, EFA6 coordinates endocytosis with cytoskeletal rearrangements.
Phytophthora pseudosyringae sp. nov., a new species causing root and collar rot of deciduous tree species in Europe.

In several studies of oak decline in Europe, a semi-papillate homothallic Phytophthora taxon was consistently isolated, together with other Phytophthora species, from rhizosphere soil samples. It was also found associated with necrotic fine roots and stem necroses of Fagus sylvatica and Alnus glutinosa. Due to morphological and physiological similarities, the semi-papillate isolates were previously identified as P. syringae by various authors. The morphology, physiology and pathogenicity against fine roots of Quercus robur, Q. petraea and F. sylvatica, bark of A. glutinosa, leaves of Ilex aquifolium and apple fruits of this Phytophthora species are described and compared with those of related and similar Phytophthora species, namely P. ilicis, P. psychrophila, P. quercina, P. citricola and P. syringae. The phylogenetic placement on the basis of ITS and mtDNA sequence data was also examined. Isolates of this taxon produce colonies with stellate to rosaceous growth patterns and limited aerial mycelium on various agar media. Antheridia are predominantly paragynous. In water culture catenulate hyphal swellings and semi-papillate caducous sporangia, that are usually limoniform, ellipsoid or ovoid, are formed abundandly, mostly in lax or dense sympodia. This taxon is a moderately slow growing, low temperature species with optimum and maximum temperatures around 20 and 25 degrees C, respectively. Tested isolates are moderately aggressive to fine roots of oaks and beech, highly aggressive to holly leaves and apple fruits, and slightly pathogenic to alder bark. Thirteen tested isolates had an identical and distinct ITS sequence which was more similar to that of P. ilicis and P. psychrophila than any other known taxa. On the basis of their unique combination of morphological characters, colony growth patterns, cardinal temperatures for growth, growth rates, pathogenicity to oaks, beech, alder, apple and holly, their host range, and ITS and mtDNA sequences the semi-papillate caducous Phytophthora isolates from oaks, beech and alder are clearly separated from related and similar Phytophthora spp. , and described as a new species, P. pseudosyringae sp. nov.
Pharmacodynamics and Atracurium and Laudanosine Concentrations during a Fixed Continuous Infusion of Atracurium in Mechanically Ventilated Patients with Acute Respiratory Distress Syndrome

The present study was designed to assess the pharmacodynamics and the plasma levels of atracurium and laudanosine found during a 72-hour fixed rate infusion of atracurium in acute respiratory distress syndrome patients without renal or liver failure. Nine sedated and mechanically ventilated acute respiratory distress syndrome patients without renal or liver failure were paralysed with a bolus of atracurium (1 mg.kg -1 ) followed by a 72-hour continuous infusion (1 mg.kg -1 .h -1 ). The count of train-of-four (TOF) and TOF ratio were monitored by an accelerograph until full neuromuscular recovery (T4/T1 0.7). Atracurium and laudanosine concentrations were measured from the onset to four days after cessation of the infusion. An electroencephalogram was recorded daily. Analysis showed that TOF count was always 3 until cessation of the infusion. Following cessation, neuromuscular recovery occurred between 31 and 96 minutes (median value=45 min). The highest atracurium and laudanosine concentrations ranged from 3.3 to 5.8 μg. ml –1 and from 3 to 20 μg. ml –1 respectively. In four patients with renal impairment, the highest laudanosine concentration was >10 μg. ml –1 . No seizure was recorded. A fixed infusion rate of atracurium in acute respiratory distress syndrome patients provided an effective muscle paralysis with a rapid neuromuscular recovery but can lead to accumulation of laudanosine in patients with renal impairment.
Diagnosis, management and prevention of ventilator‐associated pneumonia in the UK

Background and objective: Ventilator‐associated pneumonia is a nosocomial infection that occurs in patients receiving mechanical ventilation for >48 h. Many aspects of its diagnosis, treatment and management are controversial. We used a postal questionnaire to survey current practice within the UK. Methods: Questionnaire study of 207 general intensive care units in the UK. Results: The response rate was 77.3%. Regarding diagnosis, 30% of units obtained specimens from the lungs invasively, while the remainder relied on tracheal aspirates. In only 28.2% of units using tracheal aspirates were results reported in a quantitative manner. A clinical suspicion of ventilator‐associated pneumonia would lead to the administration of empirical antibiotic therapy in the majority of units (77.2%), opinion being almost equally divided on whether this should be mono (49.1%) or combination therapy (50.9%). Although most units received regular microbiology feedback (90.5%), the involvement of a microbiologist in the antibiotic decision‐making process was variable. Antibiotics were continued for a median of 7 days (inter‐quartile range 5‐8.5, range 2‐14 days). Compliance with the principal methods of ventilator‐associated pneumonia prevention was good. Conclusion: There is widespread variation in the methods used for the diagnosis of ventilator‐associated pneumonia within the UK. The majority of units rely on non‐quantitative analysis of tracheal aspirates. This technique has a high percentage of false‐positives, and suggests widespread over utilization of antibiotics. However, most agree that antibiotics should be given empirically when there is a clinical suspicion of ventilator‐associated pneumonia. The widespread introduction of ‘ventilator bundles’ appears to have ensured that most units actively take measures to prevent ventilator‐associated pneumonia.
Quantification of cytomegalovirus DNA in peripheral blood leukocytes by a branched-DNA signal amplification assay

Quantification of cytomegalovirus (CMV) DNA in blood may aid in the identification of patients at highest risk for developing CMV disease, the evaluation of new therapeutics, and the prompt recognition of drug-resistant CMV strains. A branched-DNA (bDNA) assay was developed for the reliable quantification of CMV DNA in peripheral blood leukocytes. The bDNA assay allowed for the highly specific and reproducible quantification of CMV DNA in clinical specimens. Furthermore, the bDNA assay was at least as sensitive as culture techniques and displayed a nearly 3 log10 dynamic range in quantification. Changes in CMV DNA levels measured by the bDNA assay in a human immunodeficiency virus-positive patient undergoing therapy were consistent with CMV culture, antigen, and genotype results and correlated with disease progression and resistance markers. The bDNA assay for the quantification of CMV DNA may provide a useful tool that can be used to aid physicians in monitoring disease progression, evaluating therapeutic regimens, and recognizing viral resistance and drug failure.
Pneumoperitoneum for laparoscopic cholecystectomy is not associated with compromised splanchnic circulation.

OBJECTIVE To investigate the influence of increased intra-abdominal pressure during pneumoperitoneum on splanchnic circulation. DESIGN Open study. SETTING University hospital, Sweden. SUBJECTS Five otherwise healthy patients (mean age of 34 years), undergoing laparoscopic cholecystectomy. INTERVENTIONS Arterial and hepatic vein catheterization and simultaneous arterial and hepatic vein blood gas sampling in the awake state, during anaesthesia, after the establishment of pneumoperitoneum (intra-abdominal pressure level 11-13 mmHg) and after 30 and 60 minutes of pneumoperitoneum. MAIN OUTCOME MEASURES Hepatic blood flow was estimated by the continuous infusion method and used as a measure of splanchnic blood flow. Splanchnic oxygen consumption was calculated according to the Fick principle. RESULTS AND CONCLUSION Splanchnic blood flow and splanchnic oxygen consumption were not affected by pneumoperitoneum at this level of intra-abdominal pressure.
Carbon starvation of Salmonella typhimurium does not cause a general increase of mutation rates

Mutation rates in bacteria can vary depending on the genetic target studied and the specific growth conditions of the cells. Here, two different methods were used to determine how rates of mutation to antibiotic resistance, auxotrophy, and prototrophy were influenced by carbon starvation on agar plates. The rate of mutation to rifampin resistance was increased by starvation as measured by fluctuation tests, similar to what has been reported previously for Escherichia coli. In contrast, the rates of mutation to various types of auxotrophy were unaffected or decreased as measured by both fluctuation tests and a repeated-streaking procedure. Similarly, the rates of reversion to prototrophy of his and lac nonsense and missense mutations were unaffected by starvation. Thus, mutation rates of different genetic targets can be affected differently by starvation and we conclude that carbon starvation is not generally mutagenic in Salmonella typhimurium.
Analytical model of a permanent magnet brushless DC motor with non-linear ferromagnetic material

This paper presents an analytical model for determining air-gap radial and tangential magnetic field in permanent magnet brushless dc (PMBLDC) motor. The solution is based on two-dimensional analysis in polar coordinates for radially magnetized magnet. Effects caused due to non-linear behavior of the stator ferromagnetic yoke are mainly considered. Radial and tangential magnetic field, back emf and cogging torque are calculated and are validated with finite element results. The finite element analysis demonstrates the accuracy of the developed analytical model of PMBLDC motor for no load magnetic field calculation.
Whole Exome Sequencing of Chronic Myeloid Leukemia Patients

Background: Previous studies have shown that leukemogenic chromosomal translocations, including fusions between Break point Cluster Region (BCR) and Abelson (ABL) are present in the peripheral blood of healthy individuals. The aim of this study was to gain insights into the genetic alterations other than BCR-Abl translocation in molecular level, which cause chronic myeloid leukemia (CML). Methods: We performed whole-exome sequencing on four cases representative of BCR-ABL positive CML in chronic phase of the disease. Results: We did not identify any pathogenic mutation in all known genes involved in CML or other cancers in our subjects. Nevertheless, we identified polymorphisms in related genes. Conclusion: It is the first report of exome sequencing in Philadelphia chromosome positive CML patients. We did not identify any pathogenic mutation in known cancer genes in our patients who can be due to CML pathogenesis or technical limitations.
Gfi1 Coordinates Epigenetic Repression of p21Cip/WAF1 by Recruitment of Histone Lysine Methyltransferase G9a and Histone Deacetylase 1

ABSTRACT The growth factor independent 1 (Gfi1) transcriptional regulator oncoprotein plays a crucial role in hematopoietic, inner ear, and pulmonary neuroendocrine cell development and governs cell processes as diverse as self-renewal of hematopoietic stem cells, proliferation, apoptosis, differentiation, cell fate specification, and oncogenesis. However, the molecular basis of its transcriptional functions has remained elusive. Here we show that Gfi1 recruits the histone lysine methyltransferase G9a and the histone deacetylase 1 (HDAC1) in order to modify the chromatin of genes targeted for repression by Gfi1. G9a and HDAC1 are both in a repressive complex assembled by Gfi1. Endogenous Gfi1 colocalizes with G9a, HDAC1, and K9-dimethylated histone H3. Gfi1 associates with G9a and HDAC1 on the promoter of the cell cycle regulator p21 Cip/WAF1 , resulting in an increase in K9 dimethylation at histone H3. Silencing of Gfi1 expression in myeloid cells reverses G9a and HDAC1 recruitment to p21 Cip/WAF1 and elevates its expression. These findings highlight the role of epigenetics in the regulation of development and oncogenesis by Gfi1.
Thyroid Function Abnormalities in Patients Receiving Anticancer Agents

Advances in systemic chemotherapy and radiotherapy have had a profound effect on the prognosis of patients affected by many cancer histotypes. Nonetheless, one of the main challenges for modern oncology is in improving the tolerability of these treatments. The frequency and pathophysiology of the most common side effects induced by cytotoxic agents are well known. They may be immediate or delayed in onset and prevalently involve bone marrow, gastrointestinal system, liver, and cutaneous annexes.
Evaluation of antidiabetic properties of Momordica charantia in streptozotocin induced diabetic rats using metabolomics approach

Momordica charantia, also known as bitter melon or ‘peria katak’ in Malaysia, is a member of the family Cucurbitaceae. Bitter melon is an excellent source of vitamins and minerals that made it extensively nutritious. Moreover, the seed, fruit and leave of the plant contain bioactive compounds with a wide range of biological activities that have been used in traditional medicines in the treatment of several diseases, including inflammation, infections, obesity and diabetes. The aim of this study was to evaluate changes in urinary metabolite profile of the normal, streptozotocin-induced type 1 diabetes and M. charantia treated diabetic rats using proton nuclear magnetic resonance ( 1 H-NMR) -based metabolomics profiling. Study had been carried out by inducing diabetes in the rats through injection of streptozotocin, which exhibited type 1 diabetes. M. charantia extract (100 and 200 mg/kg body weight) was administrated to the streptozotocin-induced diabetic rats for one week. Blood glucose level after administration was measured to examine hypoglycemic effect of the extract. The results obtained indicated that M. charantia was effective in lowering blood glucose level of the diabetic rats. The loading plot of Partial Least Square (PLS) component 1 showed that diabetic rats had increased levels of lactate and glucose in urine whereas normal and the extract treated diabetic rats had higher levels of succinate, creatine, creatinine, urea and phenylacetylglycine in urine. While the loading plot of PLS component 2 showed a higher levels of succinate, citrate, creatine, creatinine, sugars, and hippurate in urine of normal rat compared to the extract treated diabetic rat. Administration of M. charantia extract was found to be able to regulate the altered metabolic processes. Thus, it could be potentially used to treat the diabetic patients.
Instrumented fusion for degenerative spondylolisthesis: is it necessary?

The benefit of surgical decompression and fusion has been reasonably established for patients with degenerative spondylolisthesis and stenosis: patients who undergo fusion do better, in the long run, than those who do not undergo fusion. What has not been well established is the role of segmental spinal instrumentation in these cases. Dr. Frank Phillips, MD, provides an overview of the peer-reviewed literature in making his argument that segmental instrumentation may increase fusion rates but has not improved outcomes, despite the associated increase in cost and risk. Dr. Jeffrey Fischgrund, MD, points out the importance of patient selection in recognizing those patients at risk for pseudarthrosis, in whom spinal instrumentation will improve the chances of long-term success.
Risk Factors For Surgical Site Infection After Elective Resection of the Colon and Rectum: A Single-Center Prospective Study of 2,809 Consecutive Patients

ObjectiveTo identify the risk factors for surgical site infection (SSI) in patients undergoing elective resection of the colon and rectum. Summary Background DataSSI causes a substantial number of deaths and complications. Determining risk factors for SSI may provide information on reducing complications and improving outcome. MethodsThe authors performed a prospective study of 2,809 consecutive patients undergoing elective colorectal resection via laparotomy between February 1995 and December 1998 at a single institution. The outcome of interest was SSI, which was classified as being incisional or organ/space with or without clinical leakage. A likelihood ratio forward regression model was used to assess the independent association of variables with SSIs. ResultsThe overall SSI, incisional SSI, and organ/space SSI with and without clinical anastomotic leakage rates were 4.7%, 3%, 2%, and 0.8%, respectively. Risk factors for overall SSI were American Society of Anesthesiology (ASA) score 2 or 3 (odd ratio [OR] = 1.7), male gender (OR = 1.5), surgeons (OR = 1.3–3.3), types of operation (OR = 0.3–2.1), creation of ostomy (OR = 2.1), contaminated wound (OR = 2.9), use of drainage (OR = 1.6), and intra- or postoperative blood transfusion (1–3 units, OR = 5.3; ≥4 units, OR = 6.2). However, SSIs at specific sites differed from each other with respect to the risk factors. Among a variety of risk factors, only blood transfusion was consistently associated with a risk of SSI at any specific site. ConclusionsIn addition to ASA score and surgical wound class, blood transfusion, creation of ostomy, types of operation, use of drainage, sex, and surgeons were important in predicting SSIs after elective colorectal resection.
Land use and climatic factors structure regional patterns in soil microbial communities.

AIM Although patterns are emerging for macroorganisms, we have limited understanding of the factors determining soil microbial community composition and productivity at large spatial extents. The overall objective of this study was to discern the drivers of microbial community composition at the extent of biogeographical provinces and regions. We hypothesized that factors associated with land use and climate would drive soil microbial community composition and biomass. LOCATION Great Basin Province, Desert Province and California Floristic Province, California, USA. METHODS Using phospholipid fatty acid analysis, we compared microbial communities across eight land-use types sampled throughout the State of California, USA (n = 1117). RESULTS The main factor driving composition and microbial biomass was land-use type, especially as related to water availability and disturbance. Dry soils were more enriched in Gram-negative bacteria and fungi, and wetter soils were more enriched in Gram-positive, anaerobic and sulphate-reducing bacteria. Microbial biomass was lowest in ecosystems with the wettest and driest soils. Disturbed soils had less fungal and more Gram-positive bacterial biomass than wildland soils. However, some factors known to influence microbial communities, such as soil pH and specific plant taxa, were not important here. MAIN CONCLUSIONS Distinct microbial communities were associated with land-use types and disturbance at the regional extent. Overall, soil water availability was an important determinant of soil microbial community composition. However, because of the inclusion of managed and irrigated agricultural ecosystems, the effect of precipitation was not significant. Effects of environmental and management factors, such as flooding, tillage and irrigation, suggest that agricultural management can have larger effects on soil microbial communities than elevation and precipitation gradients.
The Trench Power MOSFET—Part II: Application Specific VDMOS, LDMOS, Packaging, and Reliability

The technological development of application specific VDMOS and lateral trench power MOSFETs is described. Unlike general-purpose trench vertical DMOS, application specific trench DMOS comprise devices merged or optimized for a specific function or characteristic. Examples include the bidirectional lithium ion battery disconnect switch, the airbag squib driver with safety redundancy, the antilock breaking systems solenoid driver with repeated avalanche operation, and various forms of synchronous rectifiers (including integrated Schottky and pseudo-Schottky operation). Trench lateral DMOS include all implant quasi-vertical, lateral trench, and lateral trench charge balanced devices. Trench power MOSFET packaging addresses multichip surface mount, DrMOS, low inductance, and clip lead packages.
The Graft Content of Donor T Cells Expressing γδTCR+ and CD4+foxp3+ Predicts the Risk of Acute Graft versus Host Disease after Transplantation of Allogeneic Peripheral Blood Stem Cells from Unrelated Donors

Purpose: Recently, high numbers of regulatory T cells within the stem cell graft were described to be associated with less graft-versus-host disease (GVHD) after related peripheral blood stem cell transplantation (PBSCT). Studies in mice also suggest a distinct role of γδTCR+ T cells in mediating GVHD. Therefore, the aim of this study was to define the yet-unknown role of regulatory and γδTCR+ T cells in human PBSCT from unrelated donors. Experimental Design: The frequency of both T-cell subsets within the graft was analyzed in 63 patients receiving unrelated allogeneic PBSCT. The respective amounts were quantified by flow cytometry and PCR and further correlated with clinical outcome. Results: The grafts contained a median of 11.2 × 106/kg CD4+foxp3+ and 9.8 × 106/kg γδTCR+ T cells, respectively. Patients receiving more CD4+foxp3+ cells had a lower cumulative incidence of acute GVHD II-IV (44% versus 65%, P = 0.03). Interestingly, in patients who received higher concentrations of donor γδTCR+ T cells, acute GVHD II-IV was more frequent (66% versus 40%, P = 0.02). In multivariate analysis, only the graft concentration of γδTCR+ T cells (P = 0.002) and a positive cytomegalovirus status of the recipient (P = 0.03) were significantly associated with the occurrence of acute GVHD II-IV. Conclusion: Graft composition of T-cell subsets seems to affect the outcome of patients receiving allogeneic PBSCT from unrelated donors. Therefore, selective manipulation or add-back of particular subsets might be a promising strategy to reduce the incidence of GVHD.
A zero-crossing based 12b 100MS/s pipelined ADC with decision boundary gap estimation calibration

This paper describes a 12-bit zero-crossing based pipeline 100-MS/s ADC. The prototype ADC, fabricated in a 90-nm CMOS process, occupies 0.32 mm2. The capacitor mismatch is calibrated by decision boundary gap estimate algorithm that runs in the background. It achieves an ENOB of 10.2 bits for a 49 MHz input signal and dissipates 6.2 mW from a 1.2V supply for a FOM of 53fJ/step.