Miracle-dz/UniFAR-FTUs huggingface dataset:
The packer filter: an efficient mechanism for user-level network code

Code to implement network protocols can be either inside the kernel of an operating system or in user-level processes. Kernel-resident code is hard to develop, debug, and maintain, but user-level implementations typically incur significant overhead and perform poorly. The performance of user-level network code depends on the mechanism used to demultiplex received packets. Demultiplexing in a user-level process increases the rate of context switches and system calls, resulting in poor performance. Demultiplexing in the kernel eliminates unnecessary overhead. This paper describes the packet filter, a kernel-resident, protocol-independent packet demultiplexer. Individual user processes have great flexibility in selecting which packets they will receive. Protocol implementations using the packet filter perform quite well, and have been in production use for several years.
An Expanded Multilocus Sequence Typing Scheme for Propionibacterium acnes: Investigation of ‘Pathogenic’, ‘Commensal’ and Antibiotic Resistant Strains

The Gram-positive bacterium Propionibacterium acnes is a member of the normal human skin microbiota and is associated with various infections and clinical conditions. There is tentative evidence to suggest that certain lineages may be associated with disease and others with health. We recently described a multilocus sequence typing scheme (MLST) for P. acnes based on seven housekeeping genes (http://pubmlst.org/pacnes). We now describe an expanded eight gene version based on six housekeeping genes and two ‘putative virulence’ genes (eMLST) that provides improved high resolution typing (91eSTs from 285 isolates), and generates phylogenies congruent with those based on whole genome analysis. When compared with the nine gene MLST scheme developed at the University of Bath, UK, and utilised by researchers at Aarhus University, Denmark, the eMLST method offers greater resolution. Using the scheme, we examined 208 isolates from disparate clinical sources, and 77 isolates from healthy skin. Acne was predominately associated with type IA1 clonal complexes CC1, CC3 and CC4; with eST1 and eST3 lineages being highly represented. In contrast, type IA2 strains were recovered at a rate similar to type IB and II organisms. Ophthalmic infections were predominately associated with type IA1 and IA2 strains, while type IB and II were more frequently recovered from soft tissue and retrieved medical devices. Strains with rRNA mutations conferring resistance to antibiotics used in acne treatment were dominated by eST3, with some evidence for intercontinental spread. In contrast, despite its high association with acne, only a small number of resistant CC1 eSTs were identified. A number of eSTs were only recovered from healthy skin, particularly eSTs representing CC72 (type II) and CC77 (type III). Collectively our data lends support to the view that pathogenic versus truly commensal lineages of P. acnes may exist. This is likely to have important therapeutic and diagnostic implications.
Impact of NRAS Mutations for Patients with Advanced Melanoma Treated with Immune Therapies

Johnson, Lovly, and colleagues performed a retrospective analysis of clinical outcomes following immunotherapy on 229 patients with melanoma with or without NRAS mutations and report that NRAS mutations in advanced melanoma correlate with increased benefit from immune-based therapies compared with other genetic subtypes. Activating NRAS mutations are found in 15% to 20% of melanomas. Immune therapies have become a mainstay in advanced melanoma treatment. We sought to evaluate whether tumor genotype (e.g., NRAS mutations) correlates with benefit from immune therapy in melanoma. We identified 229 patients with melanoma treated with immune therapies [IL2, ipilimumab, or anti-programmed cell death-1/ligand-1 (PD-1/PD-L1)] at three centers and compared clinical outcomes following immune therapy for patients with or without NRAS mutations. Of the 229 patients with melanoma, 60 had NRAS mutation, 53 had BRAF mutation, and 116 had NRAS/BRAF wild type. The NRAS-mutant cohort had superior or a trend to superior outcomes compared with the other cohorts in terms of response to first-line immune therapy (28% vs. 16%, P = 0.04), response to any line of immune therapy (32% vs. 20%, P = 0.07), clinical benefit (response + stable disease lasting ≥24 weeks; 50% vs. 31%, P < 0.01), and progression-free survival (median, 4.1 vs. 2.9 months, P = 0.09). Benefit from anti–PD-1/PD-L1 was particularly marked in the NRAS cohort (clinical benefit rate 73% vs. 35%). In an independent group of patient samples, NRAS-mutant melanoma had higher PD-L1 expression (although not statistically significant) compared with other genotypes (8/12 vs. 9/20 samples with ≥1% expression; 6/12 vs. 6/20 samples with ≥5% expression), suggesting a potential mechanism for the clinical results. This retrospective study suggests that NRAS mutations in advanced melanoma correlate with increased benefit from immune-based therapies compared with other genetic subtypes. If confirmed by prospective studies, this may be explained in part by high rates of PD-L1 expression. Cancer Immunol Res; 3(3); 288–95. ©2015 AACR.
Autoimmune Diabetes in NOD Mouse Is L3T4 T-Lymphocyte Dependent

Cultured BALB/c islets fail to function when transplanted into diabetic nonobesediabetic (NOD) mice; such grafted tissue is rapidly destroyed by disease recurrence. The cellular requirements for this graft damage are unclear. This study was designed to investigate the role of the L3T4+ T-lymphocyte subset in disease recurrence in the NOD mouse. L3T4+ T-lymphocytes were depleted by the in vivo administration of the L3T4-specific monoclonal antibody GK1.5. This treatment reduced the level of L3T4+ T-lymphocytes from an initial 43% of the peripheral blood lymphocytes to 4%. L3T4 levels remained at this low level for ∼2 wk after withdrawal of GK1.5 treatment, after which the L3T4 levels slowly began to increase in the periphery. Grafting of cultured BALB/c islet tissue into GK 1.5-treated diabetic NOD mice resulted in a rapid return to normoglycemia that persisted for 2-4 wk. The gradual return to the hyperglycemic condition roughly correlated with the reappearance of L3T4+ T-lymphocytes in the peripheral circulation. From these findings we conclude that the disease process in the NOD mouse is L3T4 T-lymphocyte dependent.
Approaching Optimality for Solving SDD Linear Systems

We present an algorithm that on input of an $n$-vertex $m$-edge weighted graph $G$ and a value $k$, produces an {\em incremental sparsifier} $\hat{G}$ with $n-1 + m/k$ edges, such that the condition number of $G$ with $\hat{G}$ is bounded above by $\tilde{O}(k\log^2 n) $, with probability $1-p$. The algorithm runs in time $$\tilde{O}((m \log{n} + n\log^2{n})\log(1/p)). $$ As a result, we obtain an algorithm that on input of an $n\times n$ symmetric diagonally dominant matrix $A$ with $m$ non-zero entries and a vector $b$, computes a vector ${x}$ satisfying $| |{x}-A^{+}b| |_A
Intravenous interferon during the anhepatic phase of liver retransplantation and prevention of recurrence of cholestatic hepatitis C virus

Cholestatic hepatitis C virus (HCV) infection post orthotopic liver transplantation is associated with a poor prognosis. We describe 2 patients who received interferon and ribavirin for cholestatic HCV infection with clearance of HCV RNA from the serum. Both developed signs of graft failure necessitating repeat orthotopic liver transplantation, and at surgery, interferon was administered during the anhepatic phase to prevent graft reinfection. Both patients are doing well with no evidence of recurrent viremia at 36 and 24 months of follow‐up after repeat transplantation, respectively. Our results suggest that in those with cholestatic HCV infection, repeat transplantation after viral clearance is feasible and can occur without reinfection of the graft, challenging the current practice of denying retransplantation for patients with cholestatic HCV. The role of anhepatic administration of interferon deserves further examination, and this combination may provide a solution in a subset of patients with an otherwise poor prognosis. Liver Transpl 13:1710–1713, 2007. © 2007 AASLD.
A new 24 h ELISA culture based method for Helicobacter pylori chemosusceptibility

Background Clarithromycin (CH) and metronidazole (MZ) are routinely used in Helicobacter pylori treatment regimes. Recently, treatment with these antibiotics has been reported to fail in >30% of patients due to increasing resistance. The common chemosusceptibility methods are cumbersome and take up to 14 days. Chemosusceptibility of H pylori is therefore rarely checked. Aim To develop a rapid susceptibility test (RST) for H pylori. Methods Preliminary experiments were performed to find a broth medium able to support the growth of H pylori in 20 h and a reliable detection method to quickly detect the amount of H pylori grown in the media. A mixture of different components was the best broth medium; ELISA was chosen as the detection technique. Performance of the new RST was compared to a gold standard (break point agar dilution method). 200 consecutive patients were tested for H pylori infection and chemosusceptibility to CH and MZ by the gold standard and RST. Results 111 patients were infected with H pylori. 105 of these were positive by both RST and the gold standard culture method; 75/105 and 68/105 strains were susceptible to CH and MZ, respectively. RST misdiagnosed 2 strains of CH and 10 strains of MZ. Conclusions A new simple and rapid chemosusceptibility test for H pylori has been validated, which is simple to perform and reduces the procedure time from 6–14 days to 24 h.
Mapping near‐surface soil moisture with RADARSAT‐1 synthetic aperture radar data

An approach for mapping near‐surface soil moisture at the watershed scale from RADARSAT‐1 synthetic aperture radar (SAR) data was developed and tested on seven RADARSAT‐1 SAR images acquired over the northern portion of the Châteauguay River Basin in southwestern Quebec, Canada, dominated by agricultural and herbaceous fields. A soil surface roughness map was first retrieved from a SAR image by inverting an empirical backscatter model with known (or assumed) soil moisture. The resulting map was then used with the backscatter model to recover near‐surface soil moisture for the remaining SAR images. Field campaigns were conducted concurrent to SAR image acquisitions to measure soil moisture and surface roughness in 24 fields. Good agreement was observed between watershed‐scale soil moisture values and measurements averaged for all sampled fields, with a correlation coefficient of 0.96 and an RMS error of 2.2%. However, considerable scatter was found between observed and SAR‐derived soil moisture estimates at the field scale. Although the generated maps reveal reasonable small‐scale soil moisture variability, no definitive conclusions could be drawn as to whether or not the proposed approach can quantify soil moisture at the field or within field scale due to insufficient ground measurements. Furrows and herbaceous and crop vegetation, which are known to affect the radar signal, appeared to have little influence on the ability to retrieve soil moisture at the watershed scale for the images analyzed in this study.
Recurrent Half-Sib Selection with Testcross Evaluation for Increased Oil Content in Soybean

Protein meal and oil are the two commodities produced from soybean [Glycine max (L.) Merr. ] that give the crop its value. Increasing seed concentrations of either or both may add value. Objectives of this study were to investigate the effectiveness of recurrent half-sib selection for increased seed oil, to evaluate the effect of tester oil content on selection response, and to investigate testcross heterosis and inbreeding depression for seed oil content. A recurrent half-sib selection system was devised for soybean and selection for increased oil content was conducted in a population for seven and three cycles using a high and a low-oil tester, respectively. The base population was a high-oil composite with gray pubescence (tt) that was segregating for nuclear genetic ms, male sterility. In summer, the base population was planted in single plant hills and bordered with the tester (Ms i Ms i TT) in a random mating block in North Carolina. About 100 to 200 random male-sterile plants with hybrid seeds were harvested. Half-sib families derived from each male-sterile plant were then grown in Puerto Rico in winter. At maturity, seeds from tawny plants (tester hybrid) were used to identify half-sib families with high-oil content. Corresponding gray plant hybrids from sib matings within the population were bulked to start the next cycle of selection. Random progenies from the base populations and selected progenies from each cycle of selection were evaluated in a replicated field experiment at three locations in North Carolina. Cycle x tester hybrids and cycle x cycle sib hybrids were also included in the tests. The results showed that oil content was significantly increased at a rate of 1.1 ± 0.2 g kg -1 cycle -1 in the high-oil tester populations but not in the low-oil tester populations. The realized heritability estimate for the high-oil tester population was 0.12 ± 0.03. Evidence of heterosis indicated that some dominance effects on oil content existed. Dominance effects may affect the evaluation accuracy of the genotypes being tested. A high-oil tester and high-oil populations may have many common alleles resulting in less dominance and more additive effects in their hybrids. Consequently, a high-oil tester can lead to better evaluation and selection precision, compared with a low-oil tester which could mask additive effects and reduce selection precision.
New methods for large dynamic range problems in planetary formation

Modern N-body techniques for planetary dynamics are generally based on symplectic algorithms specially adapted to the Kepler problem. These methods have proven very useful in studying planet formation, but typically require the time-step for all objects to be set to a small fraction of the orbital period of the innermost body. This computational expense can be prohibitive for even moderate particle number for many physically interesting scenarios, such as recent models of the formation of hot exoplanets, in which the semimajor axis of possible progenitors can vary by orders of magnitude. We present new methods which retain most of the benefits of the standard symplectic integrators but allow for radial zones with distinct time-steps. These approaches should make simulations of planetary accretion with large dynamic range tractable. As proof-of-concept, we present preliminary science results from an implementation of the algorithm as applied to an oligarchic migration scenario for forming hot Neptunes.
Outcomes of interest in evidence-based evaluations of genetic tests

Genetic tests are increasingly available for use in traditional clinical practice settings and through direct-to-consumer marketing. The need for evidence-based information and guidance on their appropriate use has never been more apparent. The independent Working Group of the Evaluation of Genomic Applications in Practice and Prevention Initiative commissions evidence-based reviews and develops recommendations to inform decision making surrounding the implementation of genetic tests and other applications of genomic technologies into clinical practice. A critical component of this analysis involves the identification and appropriate weighting of relevant health outcomes from genetic testing. Impacts of testing on morbidity and mortality are central considerations although research to document such outcomes can be challenging to conduct. In considering the broader impacts of genetic tests on the individual, familial and societal levels, psychosocial outcomes often take on increasing importance, and their systematic evaluation is a challenge for traditional methods of evidence-based review. Incorporating these types of outcomes in evidence-based processes is possible, however, and necessary to extract balanced and complete (or as complete as available data will allow) information on potential benefits and on potential harms. The framework used by the Evaluation of Genomic Applications in Practice and Prevention Working Group in considering, categorizing, and weighting health-related outcomes as applied to genomic technologies is presented here.
Analysis of effluents released from the paper industry: Approach of its impact on agricultural soil

In the present study effluents and soil samples from the nearby paper industry collected in Bhimavaram Mandal of Andhra Pradesh and analyzed for various physio-chemical parameters like pH, TDS, TSS, TRC, TVS, TS, BOD, COD, DO. The inferences were drawn on the basis of analysis. In general, a considerable decrease in the concentration of total suspended and dissolved solids, chloride, calcium, sodium, manganese and cobalt occurred during the flow of effluents downstream. The lateral seepage of paper industrial effluent to agricultural lands increased the soil pH and electrical conductivity (EC). At shorter distances from point source, the lateral seepage of effluent increased exchangeable Na and extractable Cr, Zn, Mn, Pb and Ni in soil.
Prevalence of asthma and asthma-like symptoms in Dalat Highlands, Vietnam.

INTRODUCTION No data has been reported on the prevalence of asthma in highland rural areas of Vietnam. We attempt to determine the prevalence of asthma and asthma-like symptoms in Dalat, a Vietnamese city at 1,500 m altitude, and to learn about environmental influences, patient attitudes toward diagnosis and treatment, and the prevalent general knowledge about asthma. METHODS Investigators were trained in the use of formal questionnaires. After an extensive publicity campaign by local television, the investigators randomly selected homes for interviews in 12 districts. When physician-diagnosed asthma or asthma-like symptoms were identified, all parts of the questionnaire were completed and a more detailed visit was arranged with the patients, for clinical examination, spirometry and skin tests for important allergens. RESULTS 9,984 individuals were interviewed, of whom 243 were identified as having asthma or asthma-like symptoms, giving a prevalence of 2.4 percent. Average age was 48 +/- 27 years, age at onset of asthma was 25 +/- 22 years. Hospitalisation had been required in 18.3 percent of patients during 2003. Daily asthma treatment was used by only 17 percent of patients. 34 percent used inhalers and 6 percent used nebulisation. 52.3 percent had associated atopic features. Polyvalent positive prick tests were prevalent, but no one reacted to a pollen mixture. General knowledge about asthma was lacking. CONCLUSION The prevalence of asthma and asthma-like symptoms in Dalat is low. Allergic cutaneous reactions to house mites predominate. Diagnosis and treatment of those afflicted with asthma appears to be suboptimal. The study highlights the need for further patient education and for preventative interventions for asthma sufferers in this region.
Incomplete Recovery of Myocyte Contractile Function Despite Improvement of Myocardial Architecture With Left Ventricular Assist Device Support

Background—Unloading a failing heart with a left ventricular assist device (LVAD) can improve ejection fraction (EF) and LV size; however, recovery with LVAD explantation is rare. We hypothesized that evaluation of myocyte contractility and biochemistry at the sarcomere level before and after LVAD may explain organ-level changes. Methods and Results—Paired LV tissue samples were frozen from 8 patients with nonischemic cardiomyopathy at LVAD implantation (before LVAD) and before cardiac transplantation (after LVAD). These were compared with 8 nonfailing hearts. Isolated skinned myocytes were purified and attached to a force transducer, and dimensions, maximum calcium-saturated force, calcium sensitivity, and myofilament cooperativity were assessed. Relative isoform abundance and phosphorylation levels of sarcomeric contractile proteins were measured. With LVAD support, the unloaded EF improved (10.0±1.0% to 25.6±11.0%, P=0.007), LV size decreased (LV internal dimension at end diastole, 7.6±1.2 to 4.9±1.4 cm; P<0.001), and myocyte dimensions decreased (cross-sectional area, 1247±346 to 638±254 &mgr;m2; P=0.001). Maximum calcium-saturated force improved after LVAD (3.6±0.9 to 7.3±1.8 mN/mm2, P<0.001) implantation but was still lower than in nonfailing hearts (7.3±1.8 versus 17.6±1.8 mN/mm2, P<0.001). An increase in troponin I (TnI) phosphorylation after LVAD implantation was noted, but protein kinase C phosphorylation of TnI decreased. Biochemical changes of other sarcomeric proteins were not observed after LVAD. Conclusions—There is significant improvement in LV and myocyte size with LVAD, but there is only partial recovery of EF and myocyte contractility. LVAD support was associated only with biochemical changes in TnI, suggesting that alternate mechanisms might contribute to contractile changes after LVAD and that additional interventions may be needed to alter biochemical remodeling of the sarcomere to further enhance myofilament and organ-level recovery.
Practice‐Based Research: Lessons from Community Pharmacist Participants

We designed this project to determine community pharmacists' opinions regarding the challenges and motivations of their recent participation in a pharmacy practice‐based research study. At the conclusion of a randomized, multicenter study, 87 community pharmacist‐investigators were sent a questionnaire that explored four areas: motivating factors to participate, barriers to participation, communication tools used by study coordinators, and design issues for future studies. Fifty‐eight (67%) completed questionnaires were returned. Key factors motivating participation in the study were desire to improve the profession and opportunity to learn. Time was the greatest barrier to participation. Pharmacy practice‐based research has two distinct advantages. First, it translates clinical knowledge into direct application in the community. Second, it provides needed data to demonstrate the value of enhanced pharmacy practice. Thorough understanding of pharmacists' opinions is necessary to optimize the design of future studies.
Capital Account Liberalization and Economic Performance: Survey and Synthesis

This paper surveys the literature on the effects of capital account openness and stock market liberalization on economic growth and provides a synthesis in which we reconcile some of the different results presented in the literature. Various empirical measures used to gauge the presence of controls on capital account transactions and the liberalization of equity markets are discussed. We compare detailed measures of capital account controls that attempt to capture the intensity of enforcement with other indicators that simply capture whether controls are present. A detailed review of the literature is followed by an empirical section in which we trace the divergence in published results to differences in country coverage, sample periods, indicators of liberalization, and control variables across studies. Specifically, we show that when an institutional variable such as government reputation is added to the specification, the significance of capital account openness vanishes. Also, we demonstrate that enriching the specification by allowing for nonlinearities helps explain why different studies that ignore the nonlinear nature of the relationship find different results.