Miracle-dz/UniFAR-FTUs huggingface dataset:
The alternative sigma factor, sigmaE, is critically important for the virulence of Salmonella typhimurium.

In Escherichia coli, extracytoplasmic stress is partially controlled by the alternative sigma factor, RpoE (sigmaE). In response to environmental stress or alteration in the protein content of the cell envelope, sigmaE upregulates the expression of a number of genes, including htrA. It has been shown that htrA is required for intramacrophage survival and virulence in Salmonella typhimurium. To investigate whether sigmaE-regulated genes other than htrA are involved in salmonella virulence, we inactivated the rpoE gene of S. typhimurium SL1344 by allelic exchange and compared the phenotype of the mutant (GVB311) in vitro and in vivo with its parent and an isogenic htrA mutant (BRD915). Unlike E. coli, sigmaE is not required for the growth and survival of S. typhimurium at high temperatures. However, GVB311 did display a defect in its ability to utilize carbon sources other than glucose. GVB311 was more sensitive to hydrogen peroxide, superoxide, and antimicrobial peptides than SL1344 and BRD915. Although able to invade both macrophage and epithelial cell lines normally, the rpoE mutant was defective in its ability to survive and proliferate in both cell lines. The effect of the rpoE mutation on the intracellular behavior of S. typhimurium was greater than that of the htrA mutation. Both GVB311 and BRD915 were highly attenuated in mice. Neither strain was able to kill mice via the oral route, and the 50% lethal dose (LD50) for both strains via the intravenous (i.v.) route was very high. The i.v. LD50s for SL1344, BRD915, and GVB311 were <10, 5.5 x 10(5), and 1.24 x 10(7) CFU, respectively. Growth in murine tissues after oral and i.v. inoculation was impaired for both the htrA and rpoE mutant, with the latter mutant being more severely affected. Neither mutant was able to translocate successfully from the Peyer's patches to other organs after oral infection or to proliferate in the liver and spleen after i.v. inoculation. However, the htrA mutant efficiently colonized the livers and spleens of mice infected i.v. , but the rpoE mutant did not. Previous studies have shown that salmonella htrA mutants are excellent live vaccines. In contrast, oral immunization of mice with GVB311 was unable to protect any of the mice from oral challenge with SL1344. Furthermore, i.v. immunization with a large dose ( approximately 10(6) CFU) of GVB311 protected less than half of the orally challenged mice. Thus, our results indicate that genes in the sigmaE regulon other than htrA play a critical role in the virulence and immunogenicity of S. typhimurium.
Water table drawdown shapes the depth‐dependent variations in prokaryotic diversity and structure in Zoige peatlands

ABSTRACT Microbial communities are important to ecosystem function and sensitive to hydrological dynamics. However, we lack predictable knowledge about how soil microorganisms respond to water table drawdown in different depths. This research used a high‐throughput sequencing method to determine the responses of prokaryotic communities to the changes of water table and depth on Zoige peatlands. Our results showed that water table drawdown reduced alpha diversity indices (observed species, Shannon diversity and Chao1 richness) of prokaryotic communities. Intriguingly, the reduction of diversity varied in different depths, and was statistically significant in intermediate layers (20‐30 cm and 50‐60 cm), but not in the surface (0‐10 cm) or deep layer (90‐100 cm). In deeper layers there was greater relative abundance of most anaerobic microorganisms (e.g. Chloroflexi, Planctomyctes and NC10), but lesser amounts of most aerobes (e.g. Proteobacteria and Acidobacteria). However, the vertical distribution of prokaryotic microbiota along the depth gradient was altered by water table drawdown, mainly by enriching oligotrophs (e.g. Acidobcteria) over copiotrophs (e.g. Bacteriodetes). In addition, we found that the most important soil parameters influencing community structure were soil pH, total organic carbon and total nitrogen. Our study illuminates that the variations of prokaryotic communities caused by water table drawdown are depth‐dependent, and that water table drawdown leads to predictive changes of microbiota in peatlands. &NA; Graphical Abstract Figure. Variations of prokaryotic communities caused by water table drawdown in peatlands are depth‐dependent and possibly predictive.
Minimum-Aggregate-Concave-Cost Multicommodity Flows in Strong-Series-Parallel Networks

This work develops a polynomial-time dynamic-programming algorithm for minimum-aggregate-concave-cost multicommodity flow problems in strong-series-parallel networks. Many important problems from production and inventory management, capacity planning, network design and transportation can be formulated in these terms. Our results include a characterization of extreme flows in strong-series-parallel networks and an algorithm based on this characterization that searches extreme flows efficiently to find an optimal one. The algorithm runs in time proportional to A(N + K), where A, N and K are respectively the numbers of arcs, nodes and commodities in the network, and appears to be the first to solve the problem in polynomial time. When applied to the dynamic economic-order-quantity problem, the algorithm matches the performance of that of Wagner and Whitin (1958). Moreover, our algorithm has broader applications, including the multi-division capacity expansion problem and the generalization of the dynamic economic-order-quantity problem to series-parallel production processes in which subassemblies are assembled into a finished product.
Significant Changes In The Distribution Of Histologic Types Of Lung Cancer In Hong Kong

&NA; A retrospective study of 2385 Chinese patients with proven carcinoma of lung was performed. The autopsy incidence was 3.3%. Most patients presented in the seventh decade. The age distribution was 24‐94 yrs with a mean age of 63 yrs. The four major histologic types (37.3% of adenocarcinoma, 33.4% of squamous cell carcinoma, 13.7% of small cell carcinoma and 14.7% of large cell carcinoma) accounted for 99.1% of the cases. Among the four, adenocarcinoma was the most common histologic type, particularly for females and there has been an increase in the incidence of adenocarcinoma in recent years. This trend has been observed and reported in many affluent countries. In Hong Kong, the frequency of adenocarcinoma among Chinese females is exceptionally high.
years follow-up of hip revision surgery

Revision total hip arthroplasty often presents surgeons with difficult bone loss problems. The purpose of this study was to evaluate the results of hip revision surgery according to bone stock We evaluated, in a retrospective study, 148 hip revision surgeries during 2004 to 2010. The Harris Hip Score (HHS), the acetabular cementation, the AAOS classification, the SOFCOT 99 bone loss grading and Barrack classification were used for clinical and radiological assessment. It can be observed significant improvement of HHS from a mean value of 45 preoperatively to 77.2 points postoperatively. Grade B acetabular cementation was observed in a significantly higher rate for situations that needed acetabular allograft reconstruction and where it cannot be performed because of allografts lack. Barrack grades C and D cementation were associated with 70% of SOFCOT 99 stage III and IV cases and only 5% of SOFCOT 99 stage 0-II cases.Using bone graft seems to be a reliable solution for restoring bone stock and stabilizing the cup in revision total hip arthroplasty with type II-IV acetabular defect according to the AAOS classification. Because SOFCOT 99 stages III-IV are often associated with poor cementation we prefer using uncemented distally fixed with screws revision stems for these cases.
Variability of cardiac output over time in medical intensive care unit patients

ObjectivesTo determine the amount of spontaneous variability of cardiac output over time in critically ill patients, and to determine the effect of mechanical ventilation on cardiac output variability over time. DesignCase series. SettingMedical intensive care unit in a Veterans Affairs Medical Center. PatientsTwenty-two patients with indwelling pulmonary artery flotation catheters were studied. Two patients were studied twice. InterventionsDuring a 1-hr time period in which no interventions were required or made, thermodilution cardiac output was determined at baseline and then every 15 mins for 1 hr. At each time point, five individual cardiac output measurements were made and a mean was computed. The covariables of heart rate, respiration rate, mean arterial pressure, mean pulmonary arterial pressure, pulmonary artery occlusion pressure, and temperature were also recorded at each time point. Measurements and Main ResultsThe variability of the five cardiac output measurements made at each time point was expressed by calculating for each patient a coefficient of variation of the measurements. The overall mean coefficient of variation of the measurements was 5.8%. The variability of the cardiac output measurements over time was expressed by calculating for each patient a coefficient of variation over time. The overall mean coefficient of variation over time was 7.7%. A subgroup of 15 “covariable stable‘’ patients (defined as those patients with covariables within ±5% of the mean covariable values during the hour) had a mean coefficient of variation over time of 6.4%, whereas “covariable unstable‘’ patients (with >±5% changes in any covariable) had a mean coefficient of variation over time of 9.9% (p < .05). Patients breathing spontaneously had a mean coefficient of variation over time of 10.1%, whereas mechanically ventilated patients had a mean coefficient of variation over time of 6.3% (p < .05). ConclusionsThe spontaneous variability of cardiac output should be considered when interpreting two cardiac output determinations made at separate times. Due to spontaneous variability alone, a patient with a baseline cardiac output of 10.0 L/min would be expected (95% confidence interval) to have a cardiac output range of 9.2 to 10.8 L/min if covariables were stable, and a range of at least 8.8 to 11.2 L/min if covariables were unstable. Patients who were mechanically ventilated displayed less variability than patients who were breathing spontaneously. (Crit Care Med 1994; 22:225–232)
A mixed-methods investigation to explore how women living in disadvantaged areas might be supported to improve their diets

Mixed-methods explored the potential for using Sure Start Children’s Centres (SSCCs) to deliver an intervention to improve the diets of disadvantaged women and their children. In an ‘expert’ discussion, SSCC staff described gaining women’s trust, meeting needs and bringing about change as key to engaging women successfully. Structured observations in SSCCs showed they host activities in an environment conducive to building relationships and meeting women’s needs. However, staff often missed opportunities to support women to make dietary changes. These data suggest that an intervention to help staff make the most of these opportunities would have the best chance of success.
Load Redistribution in Variable Position Wheelchairs in People With Spinal Cord Injury

Abstract Background/Objective: Tilt and recline variable position seating systems are most commonly used for pressure relief to decrease potential for skin breakdown. This study provides quantitative information on the magnitudes of loading on the seat and back during phases of tilt, recline, and standing. The objective of this study was to show that the amount of force reduction at the seat would differ across these 3 methods within their respective clinical ranges. Participants: Six able-bodied (AB) subjects (2 men, 4 women) with a median age of 25 years, and 10 subjects (8 men, 2 women) with spinal cord injury (SCI) with a median age of 35.5 years. Methods: Subjects sat on a power wheelchair with Tekscan pressure mats placed underneath a foam backrest and cushion. Data were collected at 5 positions for each method. Order of position and method tested were randomized. Linear regressions were used to calculate the relationships of normalized seat and backrest forces to seat and backrest angles for each chair configuration. Results: Normalized seat loads had strong linear relationships with the angles of change in tilt, recline, and standing for both groups. Maximum decreases in seat load occurred at full standing and full recline in the SCI subjects and in full standing in the AB subjects. Loads linearly increased on the back during tilt and recline and linearly decreased during standing for both groups. Conclusions: Standing and recline offered similar seat load reductions at their respective terminal positions. Standing also reduced loading on the backrest. Recognizing that each method had clinical benefits and drawbacks, the results of this study indicate that tilt, recline, and standing systems should be considered as a means of weight shifting for wheelchair users.
A Low PAPR Subcarrier Hopping Multiple Access with Coded OFDM for Low Latency Wireless Networks

This paper proposes a new physical layer architecture for uplink multiple access based on orthogonal frequency division multiplexing (OFDM). It achieves low peak-to-average power ratio (PAPR) and high reliability with low computational complexity at both the transmitter and receiver, targeting low-latency communications such as transmission of control information in machine-to-machine (M2M) and device-to-device (D2D) communications. Our approach is based on the judicious combination of subcarrier hopping and super-orthogonal convolutional codes (SOCC) for achieving high coding gain and frequency diversity, together with Golay complementary sequences for low PAPR signaling. By introducing non-orthogonal multiple access where the subcarriers of different users are partially overlapped, the overall bandwidth efficiency can be improved. Furthermore, the low PAPR nature improves the power efficiency and thus enhances the transmission range. Employing the successive interference cancellation at the receiver further mitigates the resulting multiple access interference.
Performance of High Breakdown Mixture Discriminant Analysis Under Different Biweight Functions

This article addresses the use of different biweight functions in high breakdown mixture discriminant analysis approach of Bashir and Carter (2005). The translated biweight S function of Rocke (1996) is used in the robust estimation of the mixture distributions parameters. As in discriminant analysis, the main purpose is to classify the test observations with greater accuracy, so the estimators producing smaller errors of misclassification are preferred. In the simulation studies, the use of Tukey's biweight function was proved to be more effective in producing better classification results as compared to the translated biweight function.
Ovarian failure in oral cyclophosphamide treatment for systemic lupus erythematosus

Ninety-two women with systemic lupus erythematosus treated with oral cyclophosphamide were studied to ascertain the prevalence and the factors associated with ovarian dysfunction. Menstrual disturbance during treatment occurred in 55% of patients: 36% had amenorrhoea and 19% had oligomenorrhoea. Sustained oligomenorrhoea occurred in 12% patients. Permanent amenorrhoea (> 12 months) after cessation of oral cyclophosphamide occurred in 27% of patients. Hormonal studies in these patients were consistent with ovarian failure. Older age at initiation of treatment and high cumulative dose of cyclophosphamide were found to be associated with this outcome. There was a trend towards linear relationship between the age of initiation of cyclophosphamide therapy and frequency of amenorrhoea. A statistically significant association between amenorrhoea and cumulative dose of cyclophosphamide after adjustment for age was found whereas no such association was linked to the duration of treatment. Fourteen of the 23 women who wished to become pregnant after cessation of treatment conceived resulting in 20 live births and two abortions.
Discriminating lysosomal membrane protein types using dynamic neural network

This work presents a dynamic artificial neural network methodology, which classifies the proteins into their classes from their sequences alone: the lysosomal membrane protein classes and the various other membranes protein classes. In this paper, neural networks-based lysosomal-associated membrane protein type prediction system is proposed. Different protein sequence representations are fused to extract the features of a protein sequence, which includes seven feature sets; amino acid (AA) composition, sequence length, hydrophobic group, electronic group, sum of hydrophobicity, R-group, and dipeptide composition. To reduce the dimensionality of the large feature vector, we applied the principal component analysis. The probabilistic neural network, generalized regression neural network, and Elman regression neural network (RNN) are used as classifiers and compared with layer recurrent network (LRN), a dynamic network. The dynamic networks have memory, i.e. its output depends not only on the input but the previous outputs also. Thus, the accuracy of LRN classifier among all other artificial neural networks comes out to be the highest. The overall accuracy of jackknife cross-validation is 93.2% for the data-set. These predicted results suggest that the method can be effectively applied to discriminate lysosomal associated membrane proteins from other membrane proteins (Type-I, Outer membrane proteins, GPI-Anchored) and Globular proteins, and it also indicates that the protein sequence representation can better reflect the core feature of membrane proteins than the classical AA composition.
Prophylaxis of venographically diagnosed deep vein thrombosis in gastrointestinal surgery. Multicentre trials 20 mg and 40 mg enoxaparin versus dextran.

OBJECTIVE To compare enoxaparin and dextran 70 for the prophylaxis of venographically diagnosed deep vein thrombosis (DVT) after gastrointestinal operations. DESIGN Part 1: randomised double blind trial; Part 2: single blind study with historical controls. SETTING Eight Norwegian hospitals. SUBJECTS 381 Patients undergoing elective gastrointestinal operations. INTERVENTIONS Part 1 (n = 329): enoxaparin 20 mg subcutaneously starting two hours before operation and continuing until the patient was fully mobilised or had had 10 injections and a placebo infusion of 0.9% sodium chloride, or dextran 70,500 ml at the start of the operation, on the evening of operation, and on the first, third, and fifth postoperative days and placebo subcutaneous injections. Part 2 (n = 52): enoxaparin 40 mg in the same regimen as part 1 (compared with 39 historical controls). Venograms 4-6 days post-operatively. MAIN OUTCOME MEASURE Venographically confirmed DVT. RESULTS Part 1: Because of the high overall incidence of DVT an interim analysis was done which showed 33/101 DVT (33%) among high risk patients in the enoxaparin 20 mg group and 33/107 (31%) in the dextran 70 group. The corresponding figures for patients at medium risk were 2/27 (7%) for enoxaparin 20 mg and 5/27 (19%) for dextran 70 (95% confidence interval (CI) for the difference--11.9 to 9.8). Part 2: the dose of enoxaparin was therefore increased to 40 mg and prophylaxis restricted to patients with cancer. There were 6/49 DVT (12%), which was compared with a random sample from the dextran 70 group from part 1 (historical controls) in which the incidence was 15/39 (38%, 95% CI of the difference 4.0 to 8.4). There were no pulmonary emboli, only 4 thrombi were above the knee and there were 4, 1 and 3 clinical DVT in the 20 mg and 40 mg enoxaparin, and dextran 70 groups, respectively. CONCLUSIONS Enoxaparin 20 mg and dextran 70 are effective prophylaxis for patients at medium risk, but enoxaparin 40 mg is required for those at high risk.
Functional Expression in Escherichia coli and Membrane Topology of Porin HopE, a Member of a Large Family of Conserved Proteins in Helicobacter pylori

ABSTRACT HopE is one of the smallest members of a family of 31 outer membrane proteins in Helicobacter pylori and has been shown to function as a porin. In this study it was cloned intoEscherichia coli where it was expressed in the outer membrane, as confirmed by indirect immunofluorescence using HopE-specific antibodies. HopE purified from E. colireconstituted channels in planar bilayer membranes that were the same size as those formed by HopE purified from H. pylori. A model of the membrane topology of HopE was constructed and indicated that this protein formed a β-barrel with 16 transmembrane amphipathic β-strands. The accuracy of this model was tested by linker insertion mutagenesis, assuming that, like other porins, amino acid insertions were not tolerated in the transmembrane β-strands but were tolerated in the adjoining loop regions. Generally, the results obtained with a series of 12 insertions of the sequence RSKDV and two substitutions were consistent with the topological model. The preponderance of amino acids that were conserved in the extended family of HopE paralogs were predicted to be within the membrane and comprised 45% of all residues in the membrane.
Thrombophilia risk factors are associated with intrauterine foetal death and pregnancy‐related venous thromboembolism

Pregnancy in healthy women is accompanied by hypercoagulable changes that may interact with thrombophilia risk factors and threaten pregnancy. However, the literature on this issue is conflicting. In investigating the relationship between pregnancy‐associated complications and the presence of thrombophilia risk factors, we studied the records of 414 women who had been examined for inherited and acquired thrombophilia in the period 1996 to 2006 because of pregnancy‐associated complications. Of a total of 885 pregnancies among the women, 397 were recorded as foetal loss/intrauterine foetal death during the first (62 %), second (25 %) or third trimester (13 %). One‐hundred‐and‐two (25 %) women had had a thromboembolic event during one of their pregnancies, and 98 (24 %) had had pre‐eclampsia on at least one occasion. Intrauterine growth restriction was found in 105 (25 %) of the women, and 29 (7 %) suffered placental abruption. We found that 120 (29 %) women had at least one thrombophilia risk factor. Factor V Leiden heterozygosity was the most common thrombophilia factor (n = 52), mostly linked with the risk of venous thromboembolism during pregnancy or postpartum and to foetal death during the second or third trimester. Fifty‐three (13 %) women had antiphospholipid antibodies (lupus anticoagulant and/or anti‐β2‐glycoprotein 1 antibodies) mainly associated with the risk of spontaneous abortion during the first trimester. In conclusion, thrombophilia was found to be considerably more common in women with pregnancy‐associated complications in comparison with the general population, and most frequently in conjunction with venous thromboembolism during pregnancy and the postpartum period.