bluuebunny/crossref_metadata_2025_split huggingface dataset:
AmaLgam+: Composing Rich Information Sources for Accurate Bug Localization
Authors: Wang Shaowei , Lo David 
Published: October 2016

AbstractDuring the evolution of a software system, a large number of bug reports are submitted. Locating the source code files that need to be fixed to resolve the bugs is a challenging problem. Thus, there is a need for a technique that can automatically figure out these buggy files. A number of bug localization solutions that take in a bug report and output a ranked list of files sorted based on their likelihood to be buggy have been proposed in the literature. However, the accuracy of these tools still needs to be improved. In this paper, to address this need, we propose AmaLgam+, which is a method for locating relevant buggy files that puts together fives sources of information, namely, version history, similar reports, structure, stack traces, and reporter information. We perform a large‐scale experiment on four open source projects, namely, AspectJ, Eclipse, SWT, and ZXing to localize more than 3000 bugs. We compare AmaLgam + with several state‐of‐the‐art approaches including AmaLgam, BLUiR+, BRtracer+, BugLocator, and TFIDF‐DHbPd. These approaches leverage one or several of the sources of information analyzed by AmaLgam+, but not all of them. On average, AmaLgam + achieves a 6.0% improvement over AmaLgam, which merges three sources of information, in terms of Mean Average Precision (MAP). For AspectJ and Eclipse datasets, in which there are many bug reports with stack traces and many reporters submit multiple bug reports, AmaLgam + achieves a 12.0% improvement over AmaLgam in terms of MAP. Compared with the other state‐of‐the‐art approaches, AmaLgam + achieves an improvement of 20.3%, 22.5%, 33.1%, and 73.9% over BLUiR+, BRtracer+, BugLocator, and TFIDF‐DHbPd in terms of MAP, respectively. Copyright © 2016 John Wiley & Sons, Ltd.
Metabolic Reconfiguration Supports Reacquisition of Primitive Phenotype in Human Mesenchymal Stem Cell Aggregates
Authors: Liu Yijun , Muñoz Nathalie , Tsai Ang-Chen , Logan Timothy M. , Ma Teng 
Published: October 2016

AbstractSpontaneous aggregation and the associated enhancement of stemness have been observed in many anchorage dependent cells. Recently, aggregation of human mesenchymal stem cells (hMSCs) in nonadherent culture has been shown to reverse expansion-induced heterogeneity and loss of stemness and reprogram the hMSC to reacquire their primitive phenotype, a phenomenon that can significantly enhance therapeutic applications of hMSC. The objective of this study was to investigate the mechanistic basis underlying the connection between multicellular aggregation and stemness enhancement in hMSC by testing the hypothesis that cellular events induced during three-dimensional aggregation on nonadherent substratum induces changes in mitochondrial metabolism that promote the expression of stem cell genes Oct4, Sox2, and Nanog. Our results show that aggregation changes mitochondrial morphology and reduces mitochondrial membrane potential, resulting in a metabolic reconfiguration characterized by increased glycolytic and anaplerotic flux, and activation of autophagy. We further demonstrate that interrupting mitochondrial respiration in two-dimensional planar culture with small molecule inhibitors partially recapitulates the aggregation-mediated enhancement in stem cell properties, whereas enhancement of mitochondrial oxidative phosphorylation in the aggregated state reduces the aggregation-induced upregulation of Oct4, Sox2, and Nanog. Our findings demonstrate that aggregation-induced metabolic reconfiguration plays a central role in reacquisition of primitive hMSC phenotypic properties.
Chemokine-Like Receptor 1 Is a Novel Wnt Target Gene that Regulates Mesenchymal Stem Cell Differentiation
Authors: Muruganandan Shanmugam , Govindarajan Rajgopal , McMullen Nichole M. , Sinal Christopher J. 
Published: October 2016

Abstract
Bone remodeling is a dynamic process requiring the coordinated action of formative (osteoblast) and resorptive (osteoclast) cell populations. An imbalance of the development and function of these cell types underlies several chronic bone loss disorders such as osteoporosis. Increased bone marrow adipocyte numbers commonly occur with bone loss disorders and numerous studies have documented an inverse relationship between bone marrow fat and bone formation. Osteoblasts and adipocytes derive in a competitive fashion from a common mesenchymal stem cell (MSC) precursor. Generally, factors that promote MSC adipogenesis inhibit osteoblastogenesis and thereby, reduce bone formation. Previously we established that the secreted protein chemerin regulates adipogenic and osteoblastogenic differentiation of MSCs by signaling through chemokine-like receptor 1 (CMKLR1). However, the fundamental mechanisms by which chemerin/CMKLR1 influences lineage determination remain largely uncharacterized. Herein, we provide experimental evidence that chemerin/CMKLR1 regulates canonical Wnt signaling in MSCs by influencing the expression, subcellular location, and transcriptional activity of the central Wnt transducer, β-catenin. Moreover, we provide evidence that CMKLR1 is a novel Wnt responsive gene that functions in a negative feedback loop to limit osteoblastogenic Wnt signaling. Mechanistically, this entails Notch-dependent changes in the expression and function of key adipogenic and osteoblastogenic transcription factors, cell cycle proteins and chromatin remodeling enzymes. Consistent with this, MSCs from CMKLR1 knockout (−/−) mice exhibited similar dependency on Notch signaling to maintain osteoblastogenic differentiation. Taken together, our findings support a fundamental biological function for chemerin/CMKLR1 to balance osteoblastogenic and adipogenic signaling and thereby contribute to the maintenance of pluripotency in MSCs.
Constitutive Activation of NIK Impairs the Self-Renewal of Hematopoietic Stem/Progenitor Cells and Induces Bone Marrow Failure
Authors: Xiu Yan , Xue Wingel Y. , Lambertz Allyn , Leidinger Mariah , Gibson-Corley Katherine , Zhao Chen 
Published: October 2016

Abstract
Previously we have shown that loss of non-canonical NF-κB signaling impairs self-renewal of hematopoietic stem/progenitor cells (HSPCs). This prompted us to investigate whether persistent activation of the non-canonical NF-κB signaling will have supportive effects on HSPC self-renewal. NF-κB-inducing kinase (NIK) is an important kinase that mainly activates the non-canonical pathway through directly phosphorylating IKKα. In contrast to our expectations, constitutive activation of NIK in the hematopoietic system leads to bone marrow (BM) failure and postnatal lethality due to intrinsic impairment of HSPC self-renewal and extrinsic disruption of BM microenvironment through enhancing osteoclastogenesis. The impaired HSPC function is associated with reduced cell proliferation and increased apoptosis and inflammatory cytokine responses. RNAseq analysis of control and NIK-activated HSPCs reveals that these effects are through non-canonical NF-κB signaling without significant changes in the canonical pathway. Gene set expression analysis of RNAseq data reveals globally decreased stem cell signature, increased maturation signature, and increased inflammatory responses. Many genes (Mpl, Tifab, Emcn, Flt3, Bcl2, and others) that regulate HSPC self-renewal, lineage commitment, and apoptosis are significantly downregulated—and those genes that regulate inflammatory responses and cell cycle inhibition (Cdkn2a and Cdkn2b) are significantly upregulated—by activation of NIK. Importantly, our data demonstrate that activation of NIK-non-canonical signaling has distinct phenotypes—smaller spleen size, decreased white blood cell counts, and reduced HSPC proliferation—compared to activation of canonical signaling. Collectively, these data indicate that the balanced non-canonical NF-κB signaling is essential for maintaining normal hematopoiesis and NIK-non-canonical signaling contributes to the development of BM failure.
Pelvic floor muscle dysfunction on 3D/4D transperineal ultrasound in patients with deep infiltrating endometriosis: a pilot study
Authors: Raimondo D. , Youssef A. , Mabrouk M. , Del Forno S. , Martelli V. , Pilu G. , Rizzo N. , Zannoni L. , Paradisi R. , Seracchioli R. 
Published: October 2016

ABSTRACTObjectivePelvic floor muscle (PFM) dysfunction seems to play an important role in the pathophysiology of pelvic pain, including that associated with deep infiltrating endometriosis (DIE). The aim of this study was to evaluate the static and dynamic morphometry of the PFM using three‐dimensional (3D) and four‐dimensional (4D) transperineal ultrasound in women with DIE compared with asymptomatic healthy women.MethodsThis was a pilot, prospective study conducted at our tertiary center between March and November 2015. Fifty nulliparous women with DIE (study group) and 35 nulliparous asymptomatic healthy women (control group) were included. 3D/4D transperineal ultrasound examination of the PFM was performed in both groups. Levator hiatal area (LHA) and anteroposterior and left–right transverse diameters were evaluated at rest, on maximum PFM contraction and on maximum Valsalva maneuver. Persistent levator ani muscle (LAM) coactivation during Valsalva maneuver was investigated.ResultsCompared with the control group, women with DIE had a smaller LHA at rest (P = 0.03) and during Valsalva maneuver (P < 0.01). Furthermore, reduction in LHA during PFM contraction (P < 0.001) and enlargement in LHA during Valsalva maneuver (P = 0.01) were significantly less marked. In comparison with controls, women with DIE presented a higher frequency of LAM coactivation during Valsalva maneuver, although this difference did not reach statistical significance (P = 0.05).Conclusions3D and 4D transperineal ultrasound is an objective and non‐invasive method for PFM morphometry and may have a role in detecting PFM dysfunction in women with DIE. Copyright © 2016 ISUOG. Published by John Wiley & Sons Ltd.
Effects of non‐rainfall water inputs on ecosystem functions
Authors: Wang Lixin , Kaseke Kudzai F. , Seely Mary K. 
Published: October 2016

Non‐rainfall water inputs (NRWIs) are the least studied hydrological components in most ecosystems. These NRWI components potentially play an important role in ecosystem dynamics and are particularly important for water‐limited systems. In this review, we summarized recent advances investigating the effects of NRWIs on various ecosystem functions, including vegetation‐water relations, biogeochemical cycling, groundwater recharge, as well as reptile and invertebrate adaptations. We also identified key knowledge gaps such as the mechanisms of NRWIs alleviating vegetation water stress, sources of the NRWI components and their quantitative contributions to ecosystem functions. To better predict the ecosystem responses to climate change especially in drylands, a better understanding and quantification of NRWI contributions is essential. WIREs Water 2017, 4:e1179. doi: 10.1002/wat2.1179This article is categorized under:

Water and Life > Nature of Freshwater Ecosystems
Science of Water > Hydrological Processes
Science of Water > Water Extremes
Wildlife monitoring with unmanned aerial vehicles: Quantifying distance to auditory detection
Authors: Scobie Corey A. , Hugenholtz Chris H. 
Published: October 2016

ABSTRACTThere is growing application of small unmanned aerial vehicles (UAVs) for detecting, enumerating, and monitoring wildlife. However, little is known about how the sound from UAVs may be affecting wildlife being studied. We quantified sound levels of 2 UAVs to determine minimum altitudes they can fly before being aurally detected by wildlife. We tested a small quadcopter (SkyRanger; Aeryon Labs, Inc., Waterloo, ON, Canada) and a fixed‐wing platform (eBee; Sensefly Ltd., Cheseaux‐sur‐Lausanne, Vaud, Switzerland) at the University of Calgary in Calgary, Alberta, Canada, between 1000 and 1200 hours on 27 September 2014. We modeled sound propagation and attenuation in relation to the lower hearing thresholds for 3 game species and 2 species of predators. Results indicate that the UAV sound levels differed in the lower frequency ranges, but were otherwise similar above 1.25 kHz. The domestic cat (Felis silvestris catus) has the lowest hearing threshold, with the capacity to hear both UAVs from the furthest distance; whereas, the mallard (Anas platyrhynchos) has the greatest hearing threshold, which means UAVs can be closer before being aurally detected. Because flying height is related to image resolution, our results indicate that the ability to detect some wildlife species may be affected by the need to fly higher to minimize sound disturbance, potentially requiring higher resolution cameras than those currently used. Also, additional flight permitting may be required if modeling indicates a UAV must fly at a greater height to avoid a behavioral response by the target species. © 2016 The Wildlife Society.
The regulatable MAL32 promoter in Saccharomyces cerevisiae: characteristics and tools to facilitate its use
Authors: Meurer Matthias , Chevyreva Veronika , Cerulus Bram , Knop Michael 
Published: October 2016

AbstractHere we describe a set of tools to facilitate the use of maltose and the MAL32 promoter for regulated gene expression in yeast, alone or in combination with the GAL1 promoter. Using fluorescent protein reporters we find that under non‐inducing conditions the MAL32 promoter exhibits a low basal level of expression, similar to the GAL1 promoter, and that both promoters can be induced independently of each other using the respective sugars, maltose and galactose. While their repression upon glucose addition is immediate and complete, we found that the MAL32 and GAL1 promoters each exhibit distinct induction kinetics. A set of plasmids is available to facilitate the application of the MAL32 promoter for chromosomal modifications using PCR targetting and for plasmid based gene expression. Copyright © 2016 John Wiley & Sons, Ltd.
Effects of Topical Atorvastatin (2 %) on Posthemorrhoidectomy Pain and Wound Healing: A Randomized Double‐Blind Placebo‐Controlled Clinical Trial
Authors: Ala Shahram , Alvandipour Mina , Saeedi Majid , Hamidian Maliheh , Shiva Afshin , Rahmani Nasrin , Faramarzi Fatemeh 
Published: October 2016

AbstractBackgroundAtorvastatin is a 3‐hydroxy‐3‐methylglutaryl coenzyme A (HMG CoA) reductase inhibitor widely used in treatment of hypercholesterolemia and prevention of coronary heart disease and has various pleiotropic effects. In this study, the efficacy of atorvastatin emulgel (2 %) in reducing postoperative pain at rest, pain during defecation and analgesic requirement after open hemorrhoidectomy was investigated.MethodsA total of 66 patients with third‐ and fourth‐degree hemorrhoids undergoing open hemorrhoidectomy were included in this prospective, double‐blind, randomized controlled trial. The patients were randomly assigned to either atorvastatin emulgel or placebo immediately after surgery and then every 12 h for 14 days. The primary outcomes were intensity of pain at rest and during defecation, measured with a visual analog scale, and the analgesic requirement, measured by amount of pethidine and acetaminophen consumption, and percent of wound healing.ResultsThere was no significant difference in the average postoperative pain scores in the first 48 h (P12h = 1, P24h = 0.128 and P48h = 0.079) after the surgery between the two groups, but at the week 1 the pain scores during defecation were considerably lower in the atorvastatin group than in placebo group (P = 0.004), which also was the same at the week 2 (P = 0.03). There was no significant difference in the average pethidine and acetaminophen (mg) administration at 12 h and 24 h between the two groups after surgery. Regarding the data about wound healing, at the week two the healing was much better in the treatment group than it was in control group and the difference was statistically significant (P = 0.04).ConclusionsCompared with placebo, atorvastatin emulgel reduced postoperative pain at rest and on defecation and could improve the healing process after open hemorrhoidectomy.Trial registration numberIRCT201404013014N8.
Role of Drain Placement in Major Hepatectomy: A NSQIP Analysis of Procedure‐Targeted Hepatectomy Cases
Authors: Shwaartz Chaya , Fields Adam C. , Aalberg Jeffrey J. , Divino Celia M. 
Published: October 2016

AbstractBackgroundThe value of drain placement in hepatic surgery has not been conclusive. The aim of this study was to determine whether drain placement during major hepatectomy was associated with negative postoperative outcomes and whether its placement reduced the need for secondary procedures.MethodsThe American College of Surgeons National Surgical Quality Improvement Program Procedure‐Targeted Hepatectomy Database was used to identify patients who underwent major hepatectomy. Patients were divided into two groups based on the placement of a drain during the procedure. Propensity score‐matched cohorts of patients who underwent major hepatic resection with or without drain placement were created accounting for patient characteristics. The primary outcomes were 30‐day postoperative complications including bile leak, post‐hepatectomy liver failure, and invasive intervention as well as mortality and readmission.ResultsA total of 1005 patients underwent major hepatectomy; 500 patients (49.8 %) had prophylactic drains placed at the conclusion of the procedure. Drain placement was associated with any complication (p < 0.001), blood transfusion (p < 0.001), renal insufficiency (p = 0.02), bile leak (p < 0.001), invasive intervention (p = 0.02), length of stay (p = 0.001), and readmission (p < 0.001). In the matched cohort, drain placement was associated with any complication (p < 0.001), blood transfusion (p < 0.001), superficial surgical site infection (SSI) (p = 0.028), bile leak (p < 0.001), and longer length of stay (0.03). In addition, placement of a prophylactic drain did not decrease the rate of postoperative bile leaks requiring therapeutic intervention (p = 0.21) (Table 2). In multivariate analysis, drain placement was independently associated with any complication (p < 0.001), blood transfusion (p = 0.02), bile leak (p < 0.001), invasive intervention (p = 0.011), superficial surgical site infection (SSI) (p = 0.039), and hospital readmission (p = 0.005) (Table 3). Placement of a prophylactic drain did not decrease the rate of postoperative bile leaks requiring therapeutic intervention (p = 0.15).ConclusionDrain placement after major hepatectomy may lead to increased postoperative complications including bile leak, superficial surgical site infection, and hospital length of stay and does not decrease the need for secondary procedures in patients with bile leaks.
Functional genomics analysis of free fatty acid production under continuous phosphate limiting conditions
Authors: Youngquist J Tyler , Korosh Travis C , Pfleger Brian F 
Published: October 2016

Abstract
Free fatty acids (FFA) are an attractive platform chemical that serves as a functional intermediate in metabolic pathways for producing oleochemicals. Many groups have established strains of Escherichia coli capable of producing various chain-length mixtures of FFA by heterologous expression of acyl-ACP thioesterases. For example, high levels of dodecanoic acid are produced by an E. coli strain expressing the Umbellularia californica FatB2 thioesterase, BTE. Prior studies achieved high dodecanoic acid yields and productivities under phosphate-limiting media conditions. In an effort to understand the metabolic and physiological changes that led to increased FFA production, the transcriptome of this strain was assessed as a function of nutrient limitation and growth rate. FFA generation under phosphate limitation led to consistent changes in transporter expression, osmoregulation, and central metabolism. Guided by these results, targeted knockouts led to a further ~11 % in yield in FFA.
Locking Plate Arthrodesis Compares Favorably with LRTI for Thumb Trapeziometacarpal Arthrosis: Early Outcomes from a Longitudinal Cohort Study
Authors: Kazmers Nikolas H. , Hippensteel K. J. , Calfee Ryan P. , Wall Lindley B. , Boyer Martin I. , Goldfarb Charles A. , Gelberman Richard H. , Osei Daniel A. 
Published: October 2016

Background Trapeziometacarpal arthrodesis (TMA) has been complicated by nonunion and hardware failure. Questions/Purposes We hypothesized that modification of the TMA technique with a locking cage plate construct would afford reliable bony union while producing greater hand function than trapeziectomy with ligament reconstruction and tendon interposition (LRTI) at early follow-up. Methods We enrolled 36 consecutive patients with trapeziometacapal osteoarthritis (14 TMA patients (15 thumbs), 22 LRTI patients (22 thumbs)). The study was powered to detect a minimal clinically important difference on the QuickDASH questionnaire between groups. Secondary outcomes included Michigan Hand Questionnaire (MHQ), VAS-pain, and EQ-5D-3L scores. Patients were examined to evaluate thumb motion and strength. TMA patients were evaluated clinically and radiographically for union. Results Mean follow-up was 15.6 months, and the mean age was 59.2 years. Union was achieved in 14/15 (93%) of TMA thumbs. Improvement in QuickDASH scores was similar after TMA and LRTI (49 to 28 and 50 to 18, respectively). Postoperative patient-rated upper extremity function, health status, and pain were similar between groups. Pinch strength was significantly greater after TMA (5.9 vs 4.7 kg). No differences in thumb or wrist range of motion were observed postoperatively with the exception of greater total metacarpophalangeal joint motion after TMA. Complications after TMA included nonunion (7%), development of symptomatic scaphotrapezotrapezoidal (STT) arthrosis (7%), symptomatic hardware (7%), and superficial branch of the radial nerve (SBRN) paresthesia (7%). Complications after LRTI included subsidence (5%), MP hyperextension deformity (5%), and SBRN paresthesias (5%). Conclusions At early follow-up, patient-rated function was similar among patients undergoing TMA and LRTI. TMA produced 25% greater pinch strength compared with LRTI. Despite historical concerns regarding global loss of ROM with arthrodesis, motion was similar between groups. Our observed TMA nonunion rate of 7% is low relative to historically reported nonunion rates (7–16%). Locking cage plate technology affords rigid fixation for TMA with promising early results noting reliable bony union while minimizing complications.
Simulating power of economic experiments: the powerBBK package
Authors: Bellemare Charles , Bissonnette Luc , Kröger Sabine 
Published: October 2016

AbstractIn this article, we highlight how simulation methods can be used to analyze power of economic experiments. We provide the powerBBK package programmed for experimental economists, that can be used to perform simulations in STATA. Power can be simulated using a single command line for various statistical tests (nonparametric and parametric), estimation methods (linear, binary, and censored regression models), treatment variables (binary, continuous, time-invariant or time varying), sample sizes, experimental periods, and other design features (within or between-subjects design). The package can be used to predict minimum sample sizes required to reach a user-specific level of power, to maximize power of a design given the researcher supplied a budget constraint, or to compute power to detect a user-specified treatment order effect in within-subjects designs. The package can also be used to compute the probability of sign errors—the probability of rejecting the null hypothesis in the wrong direction as well as the share of rejections pointing in the wrong direction. The powerBBK package is provided as an .ado file along with a help file, both of which can be downloaded here (http://www.bbktools.org).