Miracle-dz/UniFAR-FTUs huggingface dataset:
Risk factors for acute kidney injury associated with the treatment of bacterial endocarditis at a tertiary academic medical center*

Background: Acute kidney injury (AKI) is a common complication of endocarditis. Objective: To determine risk factors for the development of AKI in patients treated for endocarditis. Methods: This single centre, retrospective univariate and multivariate analysis to determine risk factors for the development of AKI included patients diagnosed with endocarditis between January 2009 and October 2013. Results: Of 211 included patients, a total of 84 (39.8%) patients developed AKI. We identified multiple independent variables associated with the development of AKI, including: age ≥ 65 years, presence of hardware, chronic kidney disease, AKI on admission, infection with Staphylococcus spp, receipt of nafcillin or oxacillin or aminoglycoside and nafcillin or oxacillin or aminoglycoside and vancomycin, vancomycin trough level ≥ 20.0 mcg/ml, aminoglycoside total daily dose reduction, duration of vancomycin exceeding three days, receipt of loop diuretic or more than three concomitant nephrotoxins and duration of loop diuretic or non-steroidal anti-inflammatory drug therapy exceeding seven days. Conclusions: In patients treated for endocarditis, multiple risk factors for AKI were identified. Prospective studies are needed to evaluate these variables for causation of AKI in patients treated for endocarditis.
Sex Determination in Insects: Variations on a Common Theme

Recent studies in a representative selection of holometabolous insects suggest that, despite diversity at the instructive level, the signal-relaying part of the sex-determining pathway is remarkably well conserved. In principle, it is composed of the transformer gene (tra), which acts as a common binary switch that transduces the selected sexual fate, female when ON, male when OFF, to the downstream effector doublesex(dsx) that controls overt sexual differentiation. An interesting recurrent feature is that tra is switched ON in the early zygote by maternally provisioned tra activity. Different male-determining signals evolved, which prevent maternal activation of zygotic tra to allow for male development. In some species, where lack of maternal activation leaves tra in the OFF state, novel female-determining signals were deployed to activate zygotic tra. It appears that both the instructive end of the pathway upstream of tra as well as the executive end downstream of dsx are primary targets of evolutionary divergence, while the transduction part seems less prone to changes. We propose that this is a feature shared with many other signaling cascades that regulate developmental fates.
Continuous Positive Airway Pressure in New-generation Mechanical Ventilators: A Lung Model Study

Background A number of new microprocessor-controlled mechanical ventilators have become available over the last few years. However, the ability of these ventilators to provide continuous positive airway pressure without imposing or performing work has never been evaluated. Methods In a spontaneously breathing lung model, the authors evaluated the Bear 1000, Drager Evita 4, Hamilton Galileo, Nellcor-Puritan-Bennett 740 and 840, Siemens Servo 300A, and Bird Products Tbird AVS at 10 cm H2O continuous positive airway pressure. Lung model compliance was 50 ml/cm H2O with a resistance of 8.2 cm H2O · l−1 · s−1, and inspiratory time was set at 1.0 s with peak inspiratory flows of 40, 60, and 80 l/min. In ventilators with both pressure and flow triggering, the response of each was evaluated. Results With all ventilators, peak inspiratory flow, lung model tidal volume, and range of pressure change (below baseline to above baseline) increased as peak flow increased. Inspiratory trigger delay time, inspiratory cycle delay time, expiratory pressure time product, and total area of pressure change were not affected by peak flow, whereas pressure change to trigger inspiration, inspiratory pressure time product, and trigger pressure time product were affected by peak flow on some ventilators. There were significant differences among ventilators on all variables evaluated, but there was little difference between pressure and flow triggering in most variables on individual ventilators except for pressure to trigger. Pressure to trigger was 3.74 ± 1.89 cm H2O (mean ± SD) in flow triggering and 4.48 ± 1.67 cm H2O in pressure triggering (P < 0.01) across all ventilators. Conclusions Most ventilators evaluated only imposed a small effort to trigger, but most also provided low-level pressure support and imposed an expiratory workload. Pressure triggering during continuous positive airway pressure does require a slightly greater pressure than flow triggering.
Two-Dimensional Forward Scattering – Comparisons of Approximate and Exact Solutions

Various methods for analyses of scattering are mentioned and new approximate relationships are derived. Experimental results for thin wire and several numerical simulations of forward scattering using approximate esti- mations, physical optics and exact solutions for two-di- mensional scattering are presented both for far and near fields. That allows not only accuracy analyses but also conclusions about scattering and total fields in the pres- ence of objects, which are important for many applications such as communications, bistatic and multistatic radars and electromagnetic compatibility.
Polyomavirus transforms rat F111 and mouse NIH 3T3 cells by different mechanisms

Polyomavirus middle tumor antigen (mT) was expressed in a line of mouse NIH 3T3 cells under control of the dexamethasone-regulatable mouse mammary tumor virus promotor. Contrary to rat F111 cells which were rendered anchorage independent by mT expression alone (L. Raptis, H. Lamfrom, and T.L. Benjamin, Mol. Cell. Biol. 5:2476-2487, 1985), mT-producing NIH 3T3 cells were unable to grow in agar even after full mT induction. The mT:pp60c-src-associated phosphatidylinositol kinase was activated in these cells to a degree similar to that in fully transformed cells expressing the small and large T antigens, in addition to mT. We therefore propose that the stimulation of this phosphatidylinositol kinase, although apparently necessary, is not sufficient for transformation of NIH 3T3 cells by polyomavirus.
Experience with inspection in ultralarge-scale development

The use of code inspection to detect errors in ultralarge software projects is discussed. In particular, quantitative results based on a 1988 study of inspection of 2.5 million lines of high-level code at Bell-Northern Research are presented. The data represent one of the largest published studies in the industry and confirm that code inspection is still one of the most efficient ways to remove software defects. How to introduce inspections in large-scale production environments successfully is described. <<ETX>>
Fractional Permissions for Race-Free Mutable References in a Dataflow Intermediate Language

ParalleX is an execution model tailored to exascale computing. To this aim, it employs a global shared memory and supports multi-level parallelism. In systems that mix parallelism and mutable shared memory, the definition of a memory model becomes challenging. Following the advice of Adve and Boehm (2010), we balance efficiency and simplicity by going the route of statically enforcing data-race freedom (DRF), which makes sequential consistency efficient to implement on weak memory models. In this paper, we report on a type system that ensures DRF for the core of the dataflow intermediate language used within ParalleX. The type system adapts the notion of fractional permissions to the dataflow context and provides a novel treatment of mutable references, using a combination of affine variables and fractional sums. We give an overview of the type system and demonstrate its use in some examples.
Unconscious discrimination of social cues from eye whites in infants

Significance The human eye with its prominent white sclera is thought to facilitate social and cooperative interactions among humans. While there is evidence for brain mechanisms that allow for the unconscious detection of eye cues in adults, it is not known whether this ability of the human brain emerges early in ontogeny and can therefore be considered a key feature of human social functioning. The current study provides neural evidence for the unconscious detection of emotion and gaze cues from the sclera in 7-mo-old infants. Our findings demonstrate the existence of fast, efficient, and reliable social cue detection mechanisms in the human infant brain that likely provide a vital foundation for the development of social interactive skills. Human eyes serve two key functions in face-to-face social interactions: they provide cues about a person’s emotional state and attentional focus (gaze direction). Both functions critically rely on the morphologically unique human sclera and have been shown to operate even in the absence of conscious awareness in adults. However, it is not known whether the ability to respond to social cues from scleral information without conscious awareness exists early in human ontogeny and can therefore be considered a foundational feature of human social functioning. In the current study, we used event-related brain potentials (ERPs) to show that 7-mo-old infants discriminate between fearful and nonfearful eyes (experiment 1) and between direct and averted gaze (experiment 2), even when presented below the perceptual threshold. These effects were specific to the human sclera and not seen in response to polarity-inverted eyes. Our results suggest that early in ontogeny the human brain detects social cues from scleral information even in the absence of conscious awareness. The current findings support the view that the human eye with its prominent sclera serves critical communicative functions during human social interactions.
A scalable processing-in-memory accelerator for parallel graph processing

The explosion of digital data and the ever-growing need for fast data analysis have made in-memory big-data processing in computer systems increasingly important. In particular, large-scale graph processing is gaining attention due to its broad applicability from social science to machine learning. However, scalable hardware design that can efficiently process large graphs in main memory is still an open problem. Ideally, cost-effective and scalable graph processing systems can be realized by building a system whose performance increases proportionally with the sizes of graphs that can be stored in the system, which is extremely challenging in conventional systems due to severe memory bandwidth limitations. In this work, we argue that the conventional concept of processing-in-memory (PIM) can be a viable solution to achieve such an objective. The key modern enabler for PIM is the recent advancement of the 3D integration technology that facilitates stacking logic and memory dies in a single package, which was not available when the PIM concept was originally examined. In order to take advantage of such a new technology to enable memory-capacity-proportional performance, we design a programmable PIM accelerator for large-scale graph processing called Tesseract. Tesseract is composed of (1) a new hardware architecture that fully utilizes the available memory bandwidth, (2) an efficient method of communication between different memory partitions, and (3) a programming interface that reflects and exploits the unique hardware design. It also includes two hardware prefetchers specialized for memory access patterns of graph processing, which operate based on the hints provided by our programming model. Our comprehensive evaluations using five state-of-the-art graph processing workloads with large real-world graphs show that the proposed architecture improves average system performance by a factor of ten and achieves 87% average energy reduction over conventional systems.
Cytochrome P450 2A13 mediates the neoplastic transformation of human bronchial epithelial cells at a low concentration of aflatoxin B1

Cytochrome P450 2A13 (CYP2A13), mainly expressed in human respiratory tract, is highly efficient in the metabolic activation of aflatoxin (AF) B1 (AFB1) and is assumed to play a role in human lung tumorigenesis in airborne AFB1 exposure. To validate the assumption, we exposed human bronchial epithelial (BEAS‐2B) cells stably expressing CYP2A13 (B‐2A13), CYP1A2 (B‐1A2) and CYP2A6 (B‐2A6) to 0.1–10 nM AFB1 for 30–50 passages. B‐2A13 cells showed increased sensitivity to 0.1 nM AFB1‐induced neoplastic transformation and the formation of tumors in nude mice were observed at passage 30 (P30) while it occurred at P50 B‐1A2 cells. B‐2A6, similar to vector control, showed no neoplastic transformation in this condition. Additionally, AFB1‐DNA adducts and 8‐OHdG significantly increased in transformed P40 B‐2A13, in parallel with the upregulation of p‐ATR, p‐BRCA1, Mre11, Rad50 and Rad51. However, the apoptosis of P40 cells was near normal, while the expression of Bax, C‐Caspase 3 and C‐PARP increased passage‐dependently. Inhibition of ATR (ATR siRNA or NU6027) reversely increased the apoptosis of P40 B‐2A13 cells in parallel with the upregulation of Bax, C‐Caspase 3 and C‐PARP, suggesting that ATR plays an important role in maintaining cell survival via antiapoptosis. Additionally, activation of ATR was necessary to neoplastic transformation since blockage of ATR in P40 cells inhibited DNA damage repair response and anchorage‐independent growth. Our data demonstrated that CYP2A13 played a critical role in AFB1‐induced neoplastic transformation. ATR‐mediated the dysfunction of apoptosis and DNA damage repair might be involved. These results help establish a linkage between airborne AFB1 and human respiratory carcinoma.
Progress in understanding electro‐mechanical signalling in the myometrium

In this review, we give a state‐of‐the‐art account of uterine contractility, focussing on excitation–contraction (electro‐mechanical) coupling (ECC). This will show how electrophysiological data and intracellular calcium measurements can be related to more modern techniques such as confocal microscopy and molecular biology, to advance our understanding of mechanical output and its modulation in the smooth muscle of the uterus, the myometrium. This new knowledge and understanding, for example concerning the role of the sarcoplasmic reticulum (SR), or stretch‐activated K channels, when linked to biochemical and molecular pathways, provides a clearer and better informed basis for the development of new drugs and targets. These are urgently needed to combat dysfunctions in excitation–contraction coupling that are clinically challenging, such as preterm labour, slow to progress labours and post‐partum haemorrhage. It remains the case that scientific progress still needs to be made in areas such as pacemaking and understanding interactions between the uterine environment and ion channel activity.
Avoiding useless mutants

Mutation testing is a program-transformation technique that injects artificial bugs to check whether the existing test suite can detect them. However, the costs of using mutation testing are usually high, hindering its use in industry. Useless mutants (equivalent and duplicated) contribute to increase costs. Previous research has focused mainly on detecting useless mutants only after they are generated and compiled. In this paper, we introduce a strategy to help developers with deriving rules to avoid the generation of useless mutants. To use our strategy, we pass as input a set of programs. For each program, we also need a passing test suite and a set of mutants. As output, our strategy yields a set of useless mutants candidates. After manually confirming that the mutants classified by our strategy as "useless" are indeed useless, we derive rules that can avoid their generation and thus decrease costs. To the best of our knowledge, we introduce 37 new rules that can avoid useless mutants right before their generation. We then implement a subset of these rules in the MUJAVA mutation testing tool. Since our rules have been derived based on artificial and small Java programs, we take our MUJAVA version embedded with our rules and execute it in industrial-scale projects. Our rules reduced the number of mutants by almost 13% on average. Our results are promising because (i) we avoid useless mutants generation; (ii) our strategy can help with identifying more rules in case we set it to use more complex Java programs; and (iii) our MUJAVA version has only a subset of the rules we derived.
Robot-assisted surgery: an emerging platform for human neuroscience research

Classic studies in human sensorimotor control use simplified tasks to uncover fundamental control strategies employed by the nervous system. Such simple tasks are critical for isolating specific features of motor, sensory, or cognitive processes, and for inferring causality between these features and observed behavioral changes. However, it remains unclear how these theories translate to complex sensorimotor tasks or to natural behaviors. Part of the difficulty in performing such experiments has been the lack of appropriate tools for measuring complex motor skills in real-world contexts. Robot-assisted surgery (RAS) provides an opportunity to overcome these challenges by enabling unobtrusive measurements of user behavior. In addition, a continuum of tasks with varying complexity—from simple tasks such as those in classic studies to highly complex tasks such as a surgical procedure—can be studied using RAS platforms. Finally, RAS includes a diverse participant population of inexperienced users all the way to expert surgeons. In this perspective, we illustrate how the characteristics of RAS systems make them compelling platforms to extend many theories in human neuroscience, as well as, to develop new theories altogether.
Indications for Penetrating Keratoplasty and Associated Procedures, 2001–2005

Purpose. To identify current indications and trends in indications for penetrating keratoplasty (PKP) and associated procedures. Methods. Retrospective chart review of all patients who underwent PKP at Wills Eye Institute from January 1, 2001, to December 31, 2005. Results. A total of 1,162 cases were performed in this 5-year period. Leading indications for PKP were pseudophakic corneal edema (PCE) in 330 (28.4%) cases, followed by regraft in 250 (22.0%), keratoconus in 186 (16%), and Fuchs’ endothelial dystrophy in 126 (10.8%) cases. Of the 330 cases of PCE, 232 (70.3%) were associated with posterior chamber intraocular lenses (PCIOLs) and 96 (29.1%) with anterior chamber lenses. In 330 eyes with PCE, the lens was not exchanged in 246 (74.5%) cases and was exchanged in 76 (23%) cases. Seventy of the exchanged lenses were anterior chamber intraocular lenses (ACIOLs) and six lenses were PCIOLs. In cases of ACIOL exchanges, 10 were for scleral sutured IOLs, 18 for PCIOLS, and 42 for another ACIOL. Conclusions. Pseudophakic corneal edema remains the leading indication for PKP at our institution followed by regraft, continuing a trend noted in our previous studies. Although the percentage of cases of PCE associated with PCIOLS increased, fewer lenses were exchanged, perhaps reflecting increased confidence in biocompatibility of newer IOLs. The decrease in overall number of corneal transplants in these 5 years continues a trend noted in our previous study and mirrors the national decline in PKP.
Causes of permanent childhood hearing impairment

The causes of Permanent Childhood Hearing Impairment (PCHI) are often quoted as being hereditary in 50%, acquired in 25%, and unknown in 25% of cases. Interest in the causes of PCHI has grown recently due to increasing diagnostic possibilities. We investigated the evidence for the reported distribution of these causes.
Evolution of flow stress in aluminium during ultra-high straining at elevated temperatures. Part II

Abstract During torsional deformation of A1 (purity 99·7%) with 0·1 or 2mm grains at 400°C and 0·2s-1, the flow curve rises to a steady-state plateau of 18 MPa for ∊ = 0·5-3·0 and then gradually decreases by 27% by ∊ = 20, after which it remains constant at about 12°5 MPa. The decrease after the traditional steady-state regime results from the formation of a final texture mainly {112} (111) which reduces the Taylor factor from 2·89 to 2·39. The subgrains remain equiaxed and constant in size from the first steady-state domain through the second. A final structure of subgrains with a third of their perimeters large-angle boundaries has the same flow stress as one with mainly dislocation walls.
Resolved Tree of Life Toward Automatic Reconstruction of a Highly

We have developed an automatable procedure for reconstructing the tree of life with branch lengths comparable across all three domains. The tree has its basis in a concatenation of 31 orthologs occurring in 191 species with sequenced genomes. It revealed interdomain discrepancies in taxonomic classification. Systematic detection and subsequent exclusion of products of horizontal gene transfer increased phylogenetic resolution, allowing us to confirm accepted relationships and resolve disputed and preliminary classifications. For example, we place the phylum Acidobacteria as a sister group of d -Proteobacteria, support a Gram-positive origin of Bacteria, and suggest a thermophilic last universal common ancestor.
Xenoestrogen-Induced ERK-1 and ERK-2 Activation via Multiple Membrane-Initiated Signaling Pathways

Xenoestrogens can mimic or antagonize the activity of physiological estrogens, and the suggested mechanism of xenoestrogen action involves binding to estrogen receptors (ERs). However, the failure of various in vitro or in vivo assays to show strong genomic activity of xenoestrogens compared with estradiol (E2) makes it difficult to explain their ability to cause abnormalities in animal (and perhaps human) reproductive functions via this pathway of steroid action. E2 has also been shown to initiate rapid intracellular signaling, such as changes in levels of intracellular calcium, cAMP, and nitric oxide, and activations of a variety of kinases, via action at the membrane. In this study, we demonstrate that several xenoestrogens can rapidly activate extracellular-regulated kinases (ERKs) in the pituitary tumor cell line GH3/B6/F10, which expresses high levels of the membrane receptor for ER-α(mER). We tested a phytoestrogen (coumestrol), organochlorine pesticides or their metabolites (endosulfan, dieldrin, and DDE), and detergent by-products of plastics manufacturing (p-nonylphenol and bisphenol A). These xenoestrogens (except bisphenol A) produced rapid (3–30 min after application), concentration (10−14–10−8 M)-dependent ERK-1/2 phosphorylation but with distinctly different activation patterns. To identify signaling pathways involved in ERK activation, we used specific inhibitors of ERs, epidermal growth factor receptors, Ca2+ signaling, Src and phosphoinositide-3 kinases, and a membrane structure disruption agent. Multiple inhibitors blocked ERK activation, suggesting simultaneous use of multiple pathways and complex signaling web interactions. However, inhibitors differentially affected each xenoestrogen response examined. These actions may help to explain the distinct abilities of xenoestrogens to disrupt reproductive functions at low concentrations.