Miracle-dz/UniFAR-FTUs huggingface dataset:
Bamboo: a data-centric, object-oriented approach to many-core software

Traditional data-oriented programming languages such as dataflow languages and stream languages provide a natural abstraction for parallel programming. In these languages, a developer focuses on the flow of data through the computation and these systems free the developer from the complexities of low-level, thread-oriented concurrency primitives. This simplification comes at a cost --- traditional data-oriented approaches restrict the mutation of state and, in practice, the types of data structures a program can effectively use. Bamboo borrows from work in typestate and software transactions to relax the traditional restrictions of data-oriented programming models to support mutation of arbitrary data structures. We have implemented a compiler for Bamboo which generates code for the TILEPro64 many-core processor. We have evaluated this implementation on six benchmarks: Tracking, a feature tracking algorithm from computer vision; KMeans, a K-means clustering algorithm; MonteCarlo, a Monte Carlo simulation; FilterBank, a multi-channel filter bank; Fractal, a Mandelbrot set computation; and Series, a Fourier series computation. We found that our compiler generated implementations that obtained speedups ranging from 26.2x to 61.6x when executed on 62 cores.
Interaction between renal prostaglandins and angiotensin II in controlling glomerular filtration in the dog.

Although previous studies suggest that the renal vasoconstrictor effects of angiotensin II (ANG II) are normally confined to the efferent arterioles, the mechanisms that prevent ANG II from constricting preglomerular vessels are still unclear. In the present study, the role of prostaglandins (PG) in protecting preglomerular vessels from ANG II constriction was examined in dogs with normal or non-filtering kidneys in which ANG II formation was blocked with captopril and renal artery pressure was servo-controlled at 75-80 mmHg. Before PG blockade (n = 6), ANG II infusion (20 ng min-1 kg-1) decreased renal blood flow (RBF) by 54 +/- 4%, but did not change glomerular filtration rate (GFR) significantly. After PG blockade (n = 6), ANG II infusion decreased GFR by 37 +/- 7% and RBF by 56 +/- 6%, while increasing calculated preglomerular resistance much more than before PG blockade. In another group of dogs, secondary changes in renal resistances, due to tubuloglomerular feedback, were prevented by occluding the ureter during mannitol diuresis until glomerular filtration ceased. After inhibition of tubuloglomerular feedback in non-filtering kidneys (n = 7), ANG II decreased RBF by 40 +/- 3% and increased glomerular hydrostatic pressure, estimated from stop-flow ureteral pressure and plasma colloid osmotic pressure, by 8.7 +/- 1.7 mmHg. Postglomerular resistance increased by 91 +/- 12% while preglomerular resistance was unchanged. (ABSTRACT TRUNCATED AT 250 WORDS)
Dosing immunotherapy combinations: Analysis of 3,526 patients for toxicity and response patterns

ABSTRACT Immunotherapy combinations are used to improve outcomes in metastatic cancer, but evidence-based knowledge of appropriate starting doses for novel combinations is lacking. Phase I-III adult combination clinical trials (≥ 1 drug was immunotherapy; anti-PD-1, PD-L1, or CTLA-4) were reviewed (PubMed Jan 1, 2010 to Sep 1, 2016; ASCO 2014–2016, ASH/ESMO 2014–2015 abstracts). The safe dose for each drug used in each combination was divided by the single-agent recommended dose to calculate dose percentage. Additive dose percentage was the sum of each dose percentage. Overall, 84 studies (N = 3,526 patients, 59 combinations) were analyzed. In 50% of studies, all drugs could be administered at full dose; 63%, in the presence of anti-PD-1/PD-L1 and 36% with anti-CTLA-4. The lowest safe starting dose for a doublet combination including a second immunotherapy was 50% of each drug; 60%, for a targeted agent. Most doublet/triplets combining anti-PD-1/PD-L1 with cytotoxics were tolerable at full doses. Response rates (median [interquartile range]) were higher for 3-drug than 2-drug combinations (53% [33–63%] (N = 23 studies) vs. 23% [14–39%]) (N = 60 studies) (p < 0.0001) with similar rates seen for targeted, cytotoxic, biologic, or additional immunotherapy combinations (p = 0.35). In conclusion, anti-PD-1/PD-L1 checkpoint inhibitors can be safely given with a variety of other immunotherapy and targeted agents, albeit at about half dose. Doublet and triplet combinations with cytotoxics could mostly be given at full doses. Anti-CTLA-4 agents compromised dosing more than anti-PD-1/PD-L1 agents. Response rates were significantly higher for 3- versus 2-drug combinations.
Testing web sites: five users is nowhere near enough

We observed the same task executed by 49 users on four production web sites. We tracked the rates of discovery of new usability problems on each site and, using that data, estimated the total number of usability problems on each site and the number of tests we would need to discover every problem. Our findings differ sharply from rules-of-thumb derived from earlier work by Virzi[1] and Nielsen[2,3] commonly viewed as "industry standards. " We found that the four sites we studied would need considerably more than five users to find 85% of the problems
Are high-level aftereffects perceptual?

Imagineanexperimentinwhichyoushowsomeonepicturesofacomputer-generatedface displaying random expressions, rang-ing from happy, through neutral, to sad.You tell the participant that she must clas-sify each picture as being either “happy”or “sad,” and you note the point onthe expression continuum at which sheswitches from mostly-“happy” classiﬁca-tions to mostly-“sad. ” Then, you ask herto repeat the task, but between each pic-ture you have her feel, with her hands butout of sight, the contours of a smiling facemask. You ﬁnd that her category bound-ary has shifted: she now classiﬁes more ofthe pictures as “sad. ” This result (reportedby Matsumiya, 2013)isanexampleofan aftereffect, in which adaptation to oneinput (the mask) has altered responsesto subsequent inputs (the images). It is“high-level” in the sense that the adaptingand test stimuli have little overlap in theirinitial sensory encoding (they are pre-sentedinseparatemodalities). Thereareatleast two ways to interpret this ﬁnding.
Vascular endothelial growth factor and angiopoietin-2 play a major role in the pathogenesis of vascular leakage in cirrhotic rats

Background and aims: The extent and molecular mechanisms governing plasma extravasation and formation of ascites in cirrhosis are unknown. Vascular endothelial growth factor-A (VEGF-A) and angiopoietin-2 (Ang-2) are endogenous substances with powerful vascular permeability effects. We assessed regional blood flow, vascular leakage, mRNA and tissular expression of VEGF-A and Ang-2 and vascular permeability following VEGF receptor 2 blockade in control and cirrhotic rats to define the vascular territories showing altered vascular permeability in cirrhosis and to determine whether VEGF-A and Ang-2 are involved in this phenomenon. Methods: Arterial blood flow was analysed with the coloured microsphere method. Vascular leakage was measured and visualised with the dye Evan’s Blue and colloidal carbon techniques, respectively. VEGF-A and Ang-2 expression were determined by real-time polymerase chain reaction (RT-PCR), immunohistochemistry and western blot. The effect on vascular permeability induced by VEGFR2 blockade was assessed by administration of the receptor inhibitor SU11248. Results: Arterial blood flow was increased in the mesentery, pancreas and small intestine but not in the kidney and spleen of cirrhotic rats as compared to controls. Increased vascular leakage was observed in the mesentery and liver, where colloidal carbon spread from microvessels to the adjacent fibrotic tracts. Increased hepatic and mesenteric expression of VEGF-A and Ang-2 was found in cirrhotic rats as compared to controls. Blockade of VEGFR2 markedly reduced hepatic and mesenteric vascular leakage in cirrhotic rats. Conclusions: Enhanced endothelial permeability is restricted to the hepatic and mesenteric vascular beds in cirrhotic rats with ascites and VEGF-A and Ang-2 are key factors in the signalling pathways regulating this dysfunction.
Beampattern-Based Tracking for Millimeter Wave Communication Systems

We present a tracking algorithm to maintain the communication link between a base station (BS) and a mobile station (MS) in a millimeter wave (mmWave) communication system, where antenna arrays are used for beamforming in both the BS and MS. Downlink transmission is considered, and the tracking is performed at the MS as it moves relative to the BS. Specifically, we consider the case that the MS rotates quickly due to hand movement. The algorithm estimates the angle of arrival (AoA) by using variations in the radiation pattern of the beam as a function of this angle. Numerical results show that the algorithm achieves accurate beam alignment when the MS rotates in a wide range of angular speeds. For example, the algorithm can support angular speeds up to 800 degrees per second when tracking updates are available every 10 ms.
Detecting ancient positive selection in humans using extended lineage sorting

Natural selection that affected modern humans early in their evolution has likely shaped some of the traits that set present-day humans apart from their closest extinct and living relatives. The ability to detect ancient natural selection in the human genome could provide insights into the molecular basis for these human-specific traits. Here, we introduce a method for detecting ancient selective sweeps by scanning for extended genomic regions where our closest extinct relatives, Neandertals and Denisovans, fall outside of the present-day human variation. Regions that are unusually long indicate the presence of lineages that reached fixation in the human population faster than expected under neutral evolution. Using simulations we show that the method is able to detect ancient events of positive selection and that it can differentiate those from background selection. Applying our method to the 1000 Genomes dataset, we find evidence for ancient selective sweeps favoring regulatory changes and present a list of genomic regions that are predicted to underlie positively selected human specific traits.
A Cluster Architecture for Embedded Perception

Recognizing speech, gestures, and visual features are important interface capabilities for future embedded mobile systems. Unfortunately the real-time performance requirements of complex perception applications can not be met by current embedded processors and often even exceed the performance of high performance microprocessors with an energy budget that is infeasible in the embedded space. The normal approach is to resort to a custom ASIC in order to meet performance and energy constraints. However ASICs incur expensive and lengthy design cycles. They are so specialized that they are unable to support multiple applications or even evolutionary improvements in a single application. This paper introduces a VLIW perception processor which uses a combination of clustered function units, compiler controlled data-flow and compiler controlled clock-gating in conjunction with hardware support for modulo scheduling, address generation units and a scratch-pad memory system to achieve very high performance for perceptual algorithms at low energy consumption. The architecture is evaluated using ten benchmark applications taken from complex speech and visual feature recognition, security, and signal processing domains. We use DSP and encryption algorithms to demonstrate that the perception processor is general enough to be applied to other streaming problems. Since energy and delay are common design tradeoffs, the energy-delay product of a CMOS implementation of this architecture is compared against ASICs and a general purpose processors. Using a combination of Spice simulations, real processor power measurements and architecture simulation we show that the cluster running at 1 GHz clock frequency outperforms a 2.4 GHz Pentium 4 by a factor of 1.75. While delivering this performance it simultaneously achieves 135 times better energy delay product than a low power Intel XScale embedded processor.
Genetic Characterization of Simian Foamy Viruses Infecting Humans

ABSTRACT Simian foamy viruses (SFVs) are retroviruses that are widespread among nonhuman primates (NHPs). SFVs actively replicate in their oral cavity and can be transmitted to humans after NHP bites, giving rise to a persistent infection even decades after primary infection. Very few data on the genetic structure of such SFVs found in humans are available. In the framework of ongoing studies searching for SFV-infected humans in south Cameroon rainforest villages, we studied 38 SFV-infected hunters whose times of infection had presumably been determined. By long-term cocultures of peripheral blood mononuclear cells with BHK-21 cells, we isolated five new SFV strains and obtained complete genomes of SFV strains from chimpanzee (Pan troglodytes troglodytes; strains BAD327 and AG15), monkey (Cercopithecus nictitans; strain AG16), and gorilla (Gorilla gorilla; strains BAK74 and BAD468). These zoonotic strains share a very high degree of similarity with their NHP counterparts and have a high degree of conservation of the genetic elements important for viral replication. Interestingly, analysis of FV DNA sequences obtained before cultivation revealed variants with deletions in both the U3 region and tas that may correlate with in vivo chronicity in humans. Genomic changes in bet (a premature stop codon) and gag were also observed. To determine if such changes were specific to zoonotic strains, we studied local SFV-infected chimpanzees and found the same genomic changes. Our study reveals that natural polymorphism of SFV strains does exist at both the intersubspecies level (gag, bet) and the intrasubspecies (U3, tas) levels but does not seem to reflect a viral adaptation specific to zoonotic SFV strains.
Effect of L-carnitine and soybean oil on growth performance and body composition of early-weaned pigs.

Two experiments were conducted to evaluate the effect of dietary L-carnitine on growth performance and body composition of early-weaned pigs. In Exp. 1, 120 weanling pigs (initially 5.6 kg and 19 +/- 2 d of age) were allotted in a 3 x 2 factorial with four pigs per pen and five replications (pens) per treatment. Main effects from d 0 to 14 after weaning included dietary L-carnitine (0, 500, or 1,000 ppm) and soybean oil (0 to 10%). From d 14 to 35 after weaning, levels were reduced to 0, 250, or 500 ppm L-carnitine and 0 or 5% soybean oil. No L-carnitine x soybean oil interactions were observed (P > .10). From d 0 to 14, L-carnitine and soybean oil had no effect (P > .10) on pig performance. From d 14 to 35 and d 0 to 35, gain:feed ratio (G/F) improved (linear, P < .05) with increasing dietary L-carnitine; however, ADG and ADFI were not affected. Soybean oil improved ADG and G/F (P < .05) from d 14 to 35 and ADG from d 0 to 35. In Exp. 2, 180 weanling pigs (initially 6.0 kg and 22 +/- 2 d of age) were allotted in a 2 x 3 factorial. Pigs were fed either 0 or 1,000 ppm L-carnitine from d 0 to 14 after weaning and then pigs fed each of these diets were fed diets containing 0, 250, or 500 ppm L-carnitine from d 14 to 35. No interactions occurred between feeding L-carnitine from d 0 to 14 and performance observed from d 14 to 35. From d 0 to 14 after weaning, L-carnitine increased ADG (P < .08) and ADFI (P < .02). From d 14 to 35, ADFI decreased (linear, P < .05) and G/F increased (quadratic, P < .05) as dietary L-carnitine increased. Cumulative (d 0 to 35) ADFI decreased (linear, P < .05) and G/F increased (linear, P < .05) with increasing L-carnitine. On d 35, 14 pigs from each of four selected treatments (0 or 1,000 ppm L-carnitine from d 0 to 14 followed by either 0 or 500 ppm from d 14 to 35) were slaughtered, and carcass composition was recorded. Carcass moisture and CP percentages were not influenced (P > .10) by dietary L-carnitine. However, pigs fed 1,000 ppm L-carnitine from d 0 to 14 had less (P < .05) carcass lipid and daily lipid accretion on d 35 whether they were fed L-carnitine from d 14 to 35 or not. These results suggest that dietary L-carnitine improves G/F and reduces carcass lipid accretion in early-weaned pigs.
SopE, a secreted protein of Salmonelladublin, is translocated into the target eukaryotic cell via a sip‐dependent mechanism and promotes bacterial entry

The entry of Salmonella into cultured epithelial cells is dependent on genes located in several adjacent chromosomal loci. One of these loci encodes the recently identified secretory proteins, denoted Sips (Salmonella invasion proteins). SipB,C,D proteins are essential for the ability of the pathogen to invade epithelial cells. To examine if additional invasion‐associated proteins were secreted by Salmonella dublin, the genes encoding already characterized secretory proteins were inactivated to facilitate this analysis. The proteins produced and secreted by a double fliM/polar sipB mutant of S. dublin were analysed; this revealed a set of novel secreted proteins. These proteins, which we denoted Sops (Salmonella outer proteins), formed large filamentous aggregates in the medium of bacterial culture growing at 37°C. These aggregates contained five predominant proteins. Here we report the identification and characterization of one of these proteins, SopE, which is a novel invasion‐associated secretory protein of S. dublin. A specific sopE mutant of S. dublin was found to be defective for invasion into epithelial cells. Upon interaction of Salmonella with HeLa cells, SopE was found to be translocated into the cytoplasm of the target cell by extracellular bacteria. The translocation of SopE was shown to be dependent on the Sip proteins because a polar sipB mutant did not translocate SopE across the HeLa cell membrane.
Pathogen Inactivation Technologies for Cellular Blood Components: an Update

Nowadays patients receiving blood components are exposed to much less transfusion-transmitted infectious diseases than three decades before when among others HIV was identified as causative agent for the acquired immunodeficiency syndrome and the transmission by blood or coagulation factors became evident. Since that time the implementation of measures for risk prevention and safety precaution was socially and politically accepted. Currently emerging pathogens like arboviruses and the well-known bacterial contamination of platelet concentrates still remain major concerns of blood safety with important clinical consequences, but very rarely with fatal outcome for the blood recipient. In contrast to the well-established pathogen inactivation strategies for fresh frozen plasma using the solvent-detergent procedure or methylene blue and visible light, the bench-to-bedside translation of novel pathogen inactivation technologies for cell-containing blood components such as platelets and red blood cells are still underway. This review summarizes the pharmacological/toxicological assessment and the inactivation efficacy against viruses, bacteria, and protozoa of each of the currently available pathogen inactivation technologies and highlights the impact of the results obtained from several randomized clinical trials and hemovigilance data. Until now in some European countries pathogen inactivation technologies are in in routine use for single-donor plasma and platelets. The invention and adaption of pathogen inactivation technologies for red blood cell units and whole blood donations suggest the universal applicability of these technologies and foster a paradigm shift in the manufacturing of safe blood.
Pathogenic diversity of Phytophthora sojae and breeding strategies to develop Phytophthora-resistant soybeans

Phytophthora stem and root rot, caused by Phytophthora sojae, is one of the most destructive diseases of soybean [Glycine max (L.) Merr. ], and the incidence of this disease has been increasing in several soybean-producing areas around the world. This presents serious limitations for soybean production, with yield losses from 4 to 100%. The most effective method to reduce damage would be to grow Phytophthora-resistant soybean cultivars, and two types of host resistance have been described. Race-specific resistance conditioned by single dominant Rps (“resistance to Phytophthora sojae”) genes and quantitatively inherited partial resistance conferred by multiple genes could both provide protection from the pathogen. Molecular markers linked to Rps genes or quantitative trait loci (QTLs) underlying partial resistance have been identified on several molecular linkage groups corresponding to chromosomes. These markers can be used to screen for Phytophthora-resistant plants rapidly and efficiently, and to combine multiple resistance genes in the same background. This paper reviews what is currently known about pathogenic races of P. sojae in the USA and Japan, selection of sources of Rps genes or minor genes providing partial resistance, and the current state and future scope of breeding Phytophthora-resistant soybean cultivars.
Chondrolysis of the Hip following Septic Arthritis: A Rare Complication of Magnetic Resonance Arthrography

Magnetic resonance arthrography (MRA) is commonly used to detect labral tears of the hip. Complications of MRA are unusual and include minor reactions such as chemical synovitis and urticaria. This paper presents a rapidly progressive chondrolysis of the hip in a young patient after arthrography. The patient had suffered from acute septic arthritis and was treated by emergent arthroscopic surgery followed by appropriate antibiotics. At 18 months of followup, there were no signs of active infection but evidence of joint chondrolysis. Magnetic resonance arthrography (MRA) of the hip is an invasive procedure and should therefore be recommended judiciously. Post-MRA pain is common but often mild and temporary, while post-MRA joint infection is rare; nevertheless, severe joint pain and limitation should raise suspicion for septic hip.
Diabetic Retinopathy: Retina‐Specific Methods for Maintenance of Diabetic Rodents and Evaluation of Vascular Histopathology and Molecular Abnormalities

Diabetic retinopathy is a major cause of visual impairment, which continues to increase in prevalence as more and more people develop diabetes. Despite the importance of vision, the retina is one of the smallest tissues in the body, and specialized techniques have been developed to study retinopathy. This article summarizes several methods used to (i) induce diabetes in mice, (ii) maintain the diabetic animals throughout the months required for development of typical vascular histopathology, (iii) evaluate vascular histopathology of diabetic retinopathy, and (iv) quantitate abnormalities implicated in the development of the retinopathy. © 2015 by John Wiley & Sons, Inc.