Miracle-dz/UniFAR-FTUs huggingface dataset:
Information needs for integration decisions in the release process of large-scale parallel development

Version control branching allows an organization to parallelize its development efforts. Releasing a software system developed in this manner requires release managers, and other project stakeholders, to make decisions about how to integrate the branched work. This group decision-making process becomes very complex in the case of large-scale parallel development. To better understand the information needs of release managers in this context, we conducted an interview study at a large software company. Our analysis of the interviews provides a view into how release managers make integration decisions, organized around ten key factors. Based on these factors, we discuss specific information needs for release managers and how the needs can be met in future work.
Consistent decrease in North Atlantic Tropical Cyclone frequency following major volcanic eruptions in the last three centuries

Injection of sulphate aerosols into the stratosphere following major volcanic eruptions alters global climate through the absorption and scattering of solar radiation. One proposed consequence is a decrease in North Atlantic Tropical Cyclone (TC) activity, as was observed following the El Chichón (1982) and Mount Pinatubo (1991) eruptions. We test this relationship using documentary and proxy reconstructions of major volcanic eruptions and TC frequency in the North Atlantic basin over the last three centuries. We find a consistent reduction in the number of TCs formed during the 3 years following major eruptions compared to the preceding 3 years, including after eruptions located at northern high latitudes. Our findings suggest that low‐latitude eruptions reduce Atlantic TC frequency by decreasing local sea surface temperatures, whereas the mechanisms for the decrease in TC frequency following high‐latitude eruptions are less clear and attribution is hampered by poor identification of these events.
MIQR: A Multilevel Incomplete QR Preconditioner for Large Sparse Least-Squares Problems

This paper describes a multilevel incomplete QR factorization for solving large sparse least-squares problems. The algorithm builds the factorization by exploiting structural orthogonality in general sparse matrices. At any given step, the algorithm finds an independent set of columns, i.e., a set of columns that have orthogonal patterns. The other columns are then block orthogonalized against columns of the independent set, and the process is repeated recursively for a certain number of levels on these remaining columns. The final level matrix is processed with a standard QR or incomplete QR factorization. Dropping strategies are employed throughout the levels in order to maintain a good level of sparsity. A few improvements to this basic scheme are explored. Among these is the relaxation of the requirement of independent sets of columns. Numerical tests are proposed which compare this scheme with the standard incomplete QR preconditioner, the robust incomplete factorization preconditioner, and the algebraic recursive multilevel solver (on normal equations).
Replication-guided nucleosome packing and nucleosome breathing expedite the formation of dense arrays

The first level of genome packaging in eukaryotic cells involves the formation of dense nucleosome arrays, with DNA coverage near 90% in yeasts. How cells achieve such high coverage within a short time, e.g. after DNA replication, remains poorly understood. It is known that random sequential adsorption of impenetrable particles on a line reaches high density extremely slowly, due to a jamming phenomenon. The nucleosome-shifting action of remodeling enzymes has been proposed as a mechanism to resolve such jams. Here, we suggest two biophysical mechanisms which assist rapid filling of DNA with nucleosomes, and we quantitatively characterize these mechanisms within mathematical models. First, we show that the ‘softness’ of nucleosomes, due to nucleosome breathing and stepwise nucleosome assembly, significantly alters the filling behavior, speeding up the process relative to ‘hard’ particles with fixed, mutually exclusive DNA footprints. Second, we explore model scenarios in which the progression of the replication fork could eliminate nucleosome jamming, either by rapid filling in its wake or via memory of the parental nucleosome positions. Taken together, our results suggest that biophysical effects promote rapid nucleosome filling, making the reassembly of densely packed nucleosomes after DNA replication a simpler task for cells than was previously thought.
Physical characteristics of subduction interface type seismogenic zones revisited

Based on global earthquake catalogs, the hypocenters, nodal planes, and seismic moments of worldwide subduction plate interface earthquakes were extracted for the period between 1900 and 2007. Assuming that the seismogenic zone coincides with the distribution of 5.5 ≤ M < 7 earthquakes, the subduction interface seismogenic zones were mapped for 80% of the trench systems and characterized with geometrical and mechanical parameters. Using this database, correlations were isolated between significant parameters to identify cause‐effect relationships. Empirical laws obtained in previous studies were revisited in light of this more complete, accurate, and uniform description of the subduction interface seismogenic zone. The seismogenic zone was usually found to end in a fore‐arc mantle, rather than at a Moho depth. The subduction velocity was the first‐order controlling parameter for variations in the physical characteristics of plate interfaces, determining both the geometry and mechanical behavior. As such, the fast subduction zones and cold slabs were associated with large and steep plate interfaces, which, in turn, had large seismic rates. The subduction velocity could not account for the potential earthquake magnitude diversity that was observed along the trenches. Events with Mw ≥ 8.5 preferentially occurred in the vicinity of slab edges, where the upper plate was continental and the back‐arc strain was neutral. This observation was interpreted in terms of compressive normal stresses along the plate interface. Large lateral ruptures should be promoted in neutral subduction zones due to moderate compressive stresses along the plate interface that allow the rupture to propagate laterally.
Wine Drinking and Risks of Cardiovascular Complications After Recent Acute Myocardial Infarction

Background—Scientific data on the clinical impact of moderate alcohol consumption after a recent acute myocardial infarction (AMI) are limited, and the specific effect of wine ethanol has not been studied. Methods and Results—In survivors of a recent AMI, we analyzed the association between ethanol intake and the risk of recurrence. The patients were classified according to the amount of ethanol that they consumed regularly during follow-up. Major prognostic factors, including the severity of the prior AMI and drug treatment, were recorded and included in the analyses. Only patients with at least 2 reliable assessments of drinking (and dietary) habits were included (n=437). The average ethanol intake was 7.6% of the total energy intake, wherein wine ethanol represented 92% of the total. Among these patients, 104 cardiovascular complications occurred during a mean follow-up period of 4 years. In comparison with abstainers, the adjusted risk of complications was reduced by 59% (95% confidence interval: 17 to 80) in patients whose average ethanol intake was 7.7% of the total energy intake (about 2 drinks/day), and by 52% (95% confidence interval: 4 to 76) in those whose average ethanol intake was of 16% of energy (about 4 drinks/day). Conclusion—Whereas moderate wine drinking was associated with a significant reduction in the risk of complications in this homogenous population of coronary heart disease patients, further studies are required to confirm the data, define the clinical and biological profile of the patients who would most benefit from wine drinking after recent AMI, and examine whether the relations found are due to ethanol or other wine ingredients.
VM-based security overkill: a lament for applied systems security research

Virtualization has seen a rebirth for a wide variety of uses; in our field, systems security researchers routinely use it as a standard tool for providing isolation and introspection. Researchers' use of virtual machines has reached a level of orthodoxy that makes it difficult for the collective wisdom to consider alternative approaches to protecting computation. We suggest that many scenarios exist where virtual machines do not provide a suitable tool or appropriate security properties. We analyze the use of virtual machines in the systems security space and we highlight other work that questions the current (ab)uses of virtualization. The takeaway message of this paper is that 'self-protection' mechanisms still represent an interesting and viable path of research. At some point, hypervisors (or whatever the lowest layer of software, firmware, or programmable hardware is) must rely on detection and protection mechanisms embedded within themselves.
Entropy waves, the zig-zag graph product, and new constant-degree expanders and extractors

The main contribution is a new type of graph product, which we call the zig-zag product. Taking a product of a large graph with a small graph, the resulting graph inherits (roughly) its size from the large one, its degree from the small one, and its expansion properties from both. Iteration yields simple explicit constructions of constant-degree expanders of every size, starting from one constant-size expander. Crucial to our intuition (and simple analysis) of the properties of this graph product is the view of expanders as functions which act as "entropy wave" propagators-they transform probability distributions in which entropy is concentrated in one area to distributions where that concentration is dissipated. In these terms, the graph product affords the constructive interference of two such waves. A variant of this product can be applied to extractors, giving the first explicit extractors whose seed length depends (poly)logarithmically on only the entropy deficiency of the source (rather than its length) and that extract almost all the entropy of high min-entropy sources. These high min-entropy extractors have several interesting applications, including the first constant-degree explicit expanders which beat the "eigenvalue bound".
Leadership and management in the undergraduate medical curriculum: a qualitative study of students’ attitudes and opinions at one UK medical school

Objective To explore undergraduate medical students’ attitudes towards and opinions about leadership and management education. Design Between 2009 and 2012 we conducted a qualitative study comprising five focus group discussions, each devoted to one of the five domains in the Medical Leadership Competency Framework, (Personal Qualities, Working with Others, Managing Services, Improving Services and Setting Direction). Each discussion examined what should be learnt, when should learning occur, what methods should be used, how should learning be assessed, what are the barriers to such education. Participants 28 students from all three clinical years (4–6) of whom 10 were women. Results 2 inter-related themes emerged: understanding the broad perspective of patients and other stakeholders involved in healthcare provision and the need to make leadership and management education relevant in the clinical context. Topics suggested by students included structure of the National Health Service (NHS), team working skills, decision-making and negotiating skills. Patient safety was seen as particularly important. Students preferred experiential learning, with placements seen as providing teaching opportunities. Structured observation, reflection, critical appraisal and analysis of mistakes at all levels were mentioned as existing opportunities for integrating leadership and management education. Students’ views about assessment and timing of such education were mixed. Student feedback figured prominently as a method of delivery and a means of assessment, while attitudes of medical professionals, students and of society in general were seen as barriers. Conclusions Medical students may be more open to leadership and management education than thought hitherto. These findings offer insights into how students view possible developments in leadership and management education and stress the importance of developing broad perspectives and clinical relevance in this context.
Identifying and discriminating between web and peer-to-peer traffic in the network core

Traffic classification is the ability to identify and categorize network traffic by application type. In this paper, we consider the problem of traffic classification in the network core.Classification at the core is challenging because only partial information about the flows and their contributors is available. We address this problem by developing a framework that can classify a flow using only unidirectional flow information. We evaluated this approach using recent packet traces that we collected and pre-classified to establish a "base truth". From our evaluation, we find that flow statistics for the server-to-client direction of a TCP connection provide greater classification accuracy than the flow statistics for the client-to-server direction. Because collection of the server-to-client flow statistics may not always be feasible, we developed and validated an algorithm that can estimate the missing statistics froma unidirectional packet trace.
Gene expression signatures and response to imatinib mesylate in gastrointestinal stromal tumor

Despite initial efficacy of imatinib mesylate in most gastrointestinal stromal tumor (GIST) patients, many experience primary/secondary drug resistance. Therefore, clinical management of GIST may benefit from further molecular characterization of tumors before and after imatinib mesylate treatment. As part of a recent phase II trial of neoadjuvant/adjuvant imatinib mesylate treatment for advanced primary and recurrent operable GISTs (Radiation Therapy Oncology Group S0132), gene expression profiling using oligonucleotide microarrays was done on tumor samples obtained before and after imatinib mesylate therapy. Patients were classified according to changes in tumor size after treatment based on computed tomography scan measurements. Gene profiling data were evaluated with Statistical Analysis of Microarrays to identify differentially expressed genes (in pretreatment GIST samples). Based on Statistical Analysis of Microarrays [False Discovery Rate (FDR), 10%], 38 genes were expressed at significantly lower levels in the pretreatment biopsy samples from tumors that significantly responded to 8 to 12 weeks of imatinib mesylate, that is, >25% tumor reduction. Eighteen of these genes encoded Krüppel-associated box (KRAB) domain containing zinc finger (ZNF) transcriptional repressors. Importantly, 10 KRAB-ZNF genes mapped to a single locus on chromosome 19p, and a subset predicted likely response to imatinib mesylate–based therapy in a naïve panel of GIST. Furthermore, we found that modifying expression of genes within this predictive signature can enhance the sensitivity of GIST cells to imatinib mesylate. Using clinical pretreatment biopsy samples from a prospective neoadjuvant phase II trial, we have identified a gene signature that includes KRAB-ZNF 91 subfamily members that may be both predictive of and functionally associated with likely response to short-term imatinib mesylate treatment. [Mol Cancer Ther 2009;8(8):2172–82]
Estimation of evapotranspiration using statistical model

The model is valid to estimate evapotranspiration using some climatic variables such as solar radiation, relative humidity and air temperature. Correlations between evapotranspiration and some climatic variables were made to investigate direct and indirect effects of these variables on evapotranspiration. The climatic variables used in the study were air temperature, relative humidity, wind speed, sunshine hours, solar radiation and cloudiness. The results showed that while air temperature, sunshine hours and solar radiation had strong and positive correlation with evapotranspiration, relative humidity and cloudiness were negatively correlated. As for the direct effects of the climatic variables on evapotranspiration, solar radiation has the highest effect (P= 0.995) followed by relative humidity (P= 0.865), air temperature (P= 0.772), cloudiness (P= 0.250), sunshine hours (P= 0.165) and wind speed (P=-0.13) in descending order. The relative contribution of each climatic variable viz solar radiation, relative humidity, air temperature, cloudiness, sunshine hours and wind speed to evapotranspiration was respectivly 31.32, 27.23%, 24.30%, 7.87%, 5.19% and 4.09%. The relative contribution of major variables showing high direct effects i.e. solar radiation, relative humidity and air temperature was used in simultaneous equations The low water potential value shown by Eq.[1] is suitable for upper Egypt. The high water potential value shown by Eq.[2] and optimal water potential value revealed by Eq.[3] are relevant to the Delta region. ++ The model was written in visual C language to be compatible with Windows 95. The model is fitted for predicting optimal water demand rates in new reclaimed land. Thus, a software package will help the decision-maker to have a prospective guideline for a water demand policy in Egypt. Abbreviations: (ETo ),Reference evapotranspiration; (ET), Evapotranspiration
High Responsivity in GaN Ultraviolet Photodetector Achieved by Growing on a Periodic Trapezoid Column-Shape Patterned Sapphire Substrate

GaN ultraviolet photodetector with metal-semiconductor-metal structure is achieved by growing on a periodic trapezoid column-shape patterned sapphire substrate using metalorganic chemical vapor deposition. Under 5-V reverse bias, the photodetector fabricated on such patterned sapphire substrate exhibits a lower dark current, a higher photocurrent, and a 476 % enhancement in the maximum responsivity as compare with those of the photodetector fabricated on conventional flat sapphire substrate. It is also found that the much larger UV-to-visible rejection ratio and the fact that responsivity drops in a smaller cut-off region are observed from photodetector fabricated by using a periodic trapezoid column-shape patterned sapphire substrate. These phenomena may all be attributed to the reduction of threading dislocation density and the improved quality of GaN film, as well as the internal reflection and/or scattering effect on the interface between GaN film and the periodic trapezoid column-shape pattern of the substrate.
Water Masers Toward Ultracompact H II Regions

We present a survey in the 616–523 rotational H2O transition toward 33 Galactic ultracompact H II regions. Maser emission is detected toward 18 of these sources; two are new detections. High-quality spectra are provided for all 18 sources. We discuss the detection rate of this survey and the correlation of various maser properties with other physical parameters. In addition, we report wide-bandwidth (316 km s-1), moderate-resolution (∼3″) H2O maser observations of the HH 80–81 region. We report the first detection of water maser emission at the approximate velocity of the molecular core. This emission is coincident with the extreme tip of the thermal jet and well removed from the much stronger and well-known maser emission at the position of VLA 3.
Podocyturia Predates Proteinuria and Clinical Features of Preeclampsia: Longitudinal Prospective Study

Podocyturia, the shedding of live podocytes, is present at delivery in women with preeclampsia. The aim of this study was to test whether podocyturia is present earlier in pregnancy and predicts for preeclampsia. We also aimed to compare test characteristics of podocyturia with those of angiogenic factors previously implicated in the pathogenesis of this disorder. We prospectively enrolled 315 women who provided blood and urine samples at the end of the second trimesters of their pregnancies (median, 27 gestational weeks) and within 24 hours of their deliveries (median, 39.5 gestational weeks). Blood samples were analyzed for angiogenic markers, including placental growth factor, the soluble receptor fms-like tyrosine kinase receptor-1 for vascular endothelial growth factor, and endoglin. The urine sediments were analyzed for podocytes, identified by staining for podocin after culturing the urinary sediments for 24 hours. This analysis included all women who developed preeclampsia (n=15), gestational hypertension (n=15), and a subsample of women who remained normotensive throughout pregnancy (n=44), matched for maternal age and number of previous pregnancies to those who developed preeclampsia. At the second trimester collection, all women who developed preeclampsia had podocyturia, compared with none of those who remained normotensive or were diagnosed with gestational hypertension. Podocyturia in the second trimester had a significantly greater sensitivity and specificity for the subsequent diagnosis of preeclampsia than any single angiogenic marker or a combination thereof. Screening for podocyturia at the end of the second trimester may allow for accurate identification of pregnant women at risk for preeclampsia.
Discovery of the eucalypt pathogen Quambalaria eucalypti infecting a non-Eucalyptus host in Uruguay

Quambalaria eucalypti, a serious pathogen of Eucalyptus, is believed to be native to Australia and introduced into various southern hemisphere countries, including Uruguay. In this study we record the discovery of Q. eucalypti causing leaf lesions on Myrceugenia glaucescens, a tree native to Uruguay. The identity of the pathogen was confirmed using DNA sequence comparisons of the internal transcribed spacer (ITS) region of the rDNA operon, as well as morphological characteristics. This is the first record of the pathogen on a host other than Eucalyptus. It clearly indicates a disturbing example of an alien invasive pathogen having undergone a host-shift from non-native Eucalyptus to a native tree in Uruguay.
Dynamics, Control, and Estimation for Aerial Robots Tethered by Cables or Bars

In this paper, we consider the problem of controlling an aerial robot connected to the ground by a passive cable or a passive rigid link. We provide a thorough characterization of this nonlinear dynamical robotic system in terms of fundamental properties such as differential flatness, controllability, and observability. We prove that the robotic system is differentially flat with respect to two output pairs: elevation of the link and attitude of the vehicle; elevation of the link and longitudinal link force (e.g., cable tension, or bar compression). We show the design of an almost globally convergent nonlinear observer of the full state that resorts only to an onboard accelerometer and a gyroscope. We also design two almost globally convergent nonlinear controllers to track any sufficiently smooth time-varying trajectory of the two output pairs. Finally, we numerically test the robustness of the proposed method in several far-from-nominal conditions: nonlinear cross-coupling effects, parameter deviations, measurements noise, and nonideal actuators.