Miracle-dz/UniFAR-FTUs huggingface dataset:
Familial rhabdoid tumour 'avant la lettre'—from pathology review to exome sequencing and back again

Here we provide compelling evidence that next‐generation sequencing will revolutionize diagnostics. We reappraised a case from 1991, published in 1993, describing the unique occurrence of an ovarian immature teratoma arising in a young woman and a clonally distinct intracerebral immature teratoma developing in her daughter. We conducted whole‐exome sequencing on constitutional DNA from the mother and her daughter and identified a previously unreported nonsense mutation (c.3533G>A; p.Trp1178*) in the chromatin remodelling gene, SMARCA4, that was present in both individuals and was subject to nonsense‐mediated decay. Tumour analysis by Sanger sequencing revealed a somatic SMARCA4 mutation in both the mother (c.2438+1G>T) and her daughter (c.3229C>T; p.Arg1077*), which are predicted to be truncating. As immature teratomas are classified as germ cell tumours, we performed a comprehensive mutation survey of 106 apparently sporadic germ cell tumours, but did not find any other clearly deleterious SMARCA4 mutations. Recently, inactivating mutations in SMARCA4 have been found in two cases of rhabdoid tumour predisposition syndrome type 2. In the light of these findings, renewed efforts to locate previously unobtainable tumour samples were successfully undertaken. Histopathological and immunohistochemical re‐analysis of the daughter's tumour revealed that it was indeed a rhabdoid tumour (atypical teratoid/rhabdoid tumour). In this context, the original pathology report of the mother's ovarian tumour was re‐interpreted as describing a malignant rhabdoid tumour of the ovary. This report raises the question as to whether molecular genetic analysis should be included in tumour classification, alongside more traditional microscopy‐based methods. The use of new sequencing technologies, particularly when applied to archived samples, will lead to many more 'molecular rediagnoses'. This is the earliest known case of rhabdoid tumour predisposition syndrome type 2 and the first described case with an autosomal dominant pattern of inheritance, only discovered through an exome sequencing project. Copyright © 2013 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
Joint Power and Resource Allocation for Block-Fading Relay-Assisted Broadcast Channels

We provide the solution for optimizing the power and resource allocation over block-fading relay-assisted broadcast channels in order to maximize the long term average achievable rates region of the users. The problem formulation assumes regenerative (repetition coding) decode-and-forward (DF) relaying strategy, long-term average total transmitted power constraint, orthogonal multiplexing of the users messages within the channel blocks, possibility to use a direct transmission (DT) mode from the base station to the user terminal directly or a relaying (DF) transmission mode, and partial channel state information. We show that our optimization problem can be transformed into an equivalent "no-relaying" broadcast channel optimization problem with each actual user substituted by two virtual users having different channel qualities and multiplexing weights. The proposed power and resource allocation strategies are expressed in closed-form that can be applied practically in centralized relay-assisted wireless networks. Furthermore, we show by numerical examples that our scheme enlarges the achievable rates region significantly.
Analysis of the Neuroinflammatory Response to TLR7 Stimulation in the Brain: Comparison of Multiple TLR7 and/or TLR8 Agonists1

Activation of astrocytes and microglia and the production of proinflammatory cytokines and chemokines are often associated with virus infection in the CNS as well as a number of neurological diseases of unknown etiology. These inflammatory responses may be initiated by recognition of pathogen-associated molecular patterns (PAMPs) that stimulate TLRs. TLR7 and TLR8 were identified as eliciting antiviral effects when stimulated by viral ssRNA. In the present study, we examined the potential of TLR7 and/or TLR8 agonists to induce glial activation and neuroinflammation in the CNS by intracerebroventricular inoculation of TLR7 and/or TLR8 agonists in newborn mice. The TLR7 agonist imiquimod induced astrocyte activation and up-regulation of proinflammatory cytokines and chemokines, including IFN-β, TNF, CCL2, and CXCL10. However, these responses were only of short duration when compared with responses induced by the TLR4 agonist LPS. Interestingly, some of the TLR7 and/or TLR8 agonists differed in their ability to activate glial cells as evidenced by their ability to induce cytokine and chemokine expression both in vivo and in vitro. Thus, TLR7 stimulation can induce neuroinflammatory responses in the brain, but individual TLR7 agonists may differ in their ability to stimulate cells of the CNS.
Capillary and venous blood glucose concentrations measured during intravenous insulin and glucose infusion: a comparison of steady and dynamic states.

BACKGROUND Patients undergoing intensive insulin therapy may have blood glucose (BG) samples drawn from arterial, capillary, or venous sources. This study compared capillary and venous BG across a range of glucose concentrations and under conditions of rapid change in BG. METHODS Following a 10-h fast, 40 adult patients with type 1 or 2 diabetes were connected to an automated glucose clamp device (Biostator, Miles Laboratories, Inc., Elkhart, IN) that induced a series of BG plateaus (hypoglycemic, euglycemic, hyperglycemic) and dynamic-state transitions (increasing, decreasing). Venous and capillary BG measurements were performed at different test points. Venous readings were adjusted to compensate for small time delays in obtaining the two samples. RESULTS Adjusted venous and capillary BG measurements were strongly correlated (R = 0.84; P < 0.0001). The bias between BG sources showed a weak but significant correlation with rate of BG change in the hypoglycemic range (P = 0.0282) but not in euglycemic or hyperglycemic BG ranges. The bias observed during dynamic conditions was two to three times larger than that observed during steady states. During rapid increases and decreases in BG (>2 mg/dL/min), 91.1% and 84.1% of paired capillary and venous results (n = 125), respectively, fell into Zone A of the consensus error grid versus 97.5% at slower rates. CONCLUSIONS Capillary and venous BG values are similar under steady-state conditions but may differ under dynamic conditions. Variability associated with these differences was substantial during all states. As hospital insulin infusion protocols are widely implemented, healthcare providers need to be aware that glucose values may differ when blood is sampled from capillary and venous sites. Based on the tight ranges used in these protocols, these differences may impact insulin dosing decisions.
Risk factor associations with wheezing patterns in children followed longitudinally from birth to 3(1/2) years.

BACKGROUND There is a paucity of detailed longitudinal data on wheeze in early childhood. Not all children who wheeze in early infancy will continue to wheeze into childhood and beyond. This study aims to investigate possible risk factors for different patterns of wheeze in the pre-school years. SUBJECTS AND METHODS Study participants were part of the Avon Longitudinal Study of Parents and Children (ALSPAC). Maternal reports of child wheeze between birth and 6 months and again between 30 and 42 months were gathered prospectively. Children were categorized into early wheeze, persistent wheeze or late onset wheeze. A large number of risk factors were assessed for each wheezing phenotype using multivariable logistic regression models. RESULTS Over 70% of children who wheezed in the first 6 months did not wheeze 3 years later. Wheezing between 0-6 months was independently associated with the presence of older siblings, male sex, delivery between April and December, bottle feeding, young maternal age, prenatal tobacco smoke exposure, atopy and parental history of asthma. From within this group of early wheezers, risk factors for wheeze that persisted beyond 6 months included pre-term delivery, young maternal age, living in rented local authority housing, atopy and a maternal (not paternal) history of asthma. Atopy and a family history of asthma emerged as the main predictors of wheeze that developed after 6 months of age. CONCLUSION It is clear that a number of wheezing syndromes exist by 3(1/2) years, albeit with some degree of overlap. Detailed follow-up of this cohort is underway to determine whether risk factor associations determined in the first 3(1/2) years have long-term significance for the clinical entity termed 'asthma'.
Alleviating the Antagonistic Effect of Moisture Stress on Smooth Crabgrass (Digitaria ischaemum) Control with Fenoxaprop

The influence of moisture stress intensity and duration, as well as tank mixtures with pendimethalin, which mitigated the antagonistic effects of drought, on fenoxaprop efficacy were evaluated. In growth chamber tests, specific soil matric potential (Ψm) levels of −0.01 to −1 MPa were imposed and maintained using a polyethylene glycol semipermeable membrane system. Moisture stress was alleviated by irrigation 48 or 96 h after herbicide treatment. Fenoxaprop efficacy was influenced by moisture stress intensity, posttreatment stress duration, and application rate. Under conditions of mild stress (Ψ ≥ −0.2 MPa), both increased application rate and irrigation 48 h after treatment alleviated the effects of drought on fenoxaprop efficacy. Under moderate stress (Ψm = −4.4 MPa), the antagonistic effects of drought were alleviated by a combination of increased rate and irrigation 48 h after treatment However, under more severe stress (Ψm ≤ −0.8 MPa), irrigation coupled with increased rate did not increase crabgrass control above 50%. Where irrigation within 48 h of treatment is not feasible, tank mixes of fenoxaprop with pendimethalin were shown to enhance smooth crabgrass control. Field lysimeter tests indicated that under moisture stress, Ψm of −0.7 MPa, smooth crabgrass shoot dry weight was reduced 65 to 94% with tank-mix combinations of ≥ 0.27 kg ai ha−1 fenoxaprop plus ≥ 2.2 kg ai ha−1 pendimethalin. These rate combinations were shown to be synergistic and able to alleviate the antagonistic effect of moisture stress on fenoxaprop efficacy.
Analgesic effect of topical sodium diclofenac 0.1% drops during retinal laser photocoagulation

AIMS To evaluate the analgesic effect of topical sodium diclofenac 0.1% during retinal laser photocoagulation. METHODS 87 patients, 45 with proliferative diabetic retinopathy treated with two sessions of panretinal photocoagulation (group A), and 42 patients with non-proliferative diabetic retinopathy who underwent grid treatment of the posterior pole (19 bilaterally) (group B). Sodium diclofenac 0.1% or sodium chloride 0.9% drops were topically applied 30–135 minutes before laser treatment in a masked fashion. Patients who had two sessions were given the alternate drug in the second one. Pain level was evaluated immediately after laser treatment with the visual analogue scale (VAS). The results were statistically analysed. RESULTS Patients in group A reported pain in 85/90 sessions (94%). The average pain level was 44.2% with sodium diclofenac 0.1% drops and 53.1% with sodium chloride 0.9% drops (p = 0.011 by paired ttest). Patients in group B reported pain in only 16/60 sessions (26.7%), and the pain level ranged from 10% to 60% regardless of the kind of drops used. There was no correlation in either group between level of pain and time interval from application of the drops to laser treatment (30–135 minutes) or average energy level used (100–500 mW). CONCLUSION Sodium diclofenac 0.1% is useful for pain reduction and should be applied before panretinal photocoagulation.
A Stochastic Nonconvex Splitting Method for Symmetric Nonnegative Matrix Factorization

Symmetric nonnegative matrix factorization (SymNMF) plays an important role in applications of many data analytics problems such as community detection, document clustering and image segmentation. In this paper, we consider a stochastic SymNMF problem in which the observation matrix is generated in a random and sequential manner. We propose a stochastic nonconvex splitting method, which not only guarantees convergence to the set of stationary points of the problem (in the mean-square sense), but further achieves a sublinear convergence rate. Numerical results show that for clustering problems over both synthetic and real world datasets, the proposed algorithm converges quickly to the set of stationary points.
Measuring Information System Service Quality: SERVQUAL from the Other Side

There has been much debate as of late over the use of the SERVQUAL instrument to measure Information Systems service quality. Detractors argue that the difference score leads to unreliable measures and that the dimensionality and validity is erratic. Proponents argue for the diagnostic power of the gap between expectations and perceived delivery while demonstrating some empirical stability and reliability. To extend the discussion requires the examination of the instrument from the viewpoint of the information system professional. Importantly, a large variety of samples must view the instrument and measures in the same light for the instrument to have applicability. Likewise, analysis of differences between users and providers requires that both populations have similar structural views of the instrument. Empirical evidence collected from information system professionals demonstrated a structure similar to previously published studies with adequate reliability, convergent validity, and discriminant validity. The structure is the same as is found for a gap between users and IS professionals.
Exhaled Nitric Oxide: A Novel Biomarker of Adverse Respiratory Health Effects in Epidemiological Studies

Abstract The sampling of exhaled breath is a noninvasive procedure that can be performed easily in adults, children, and patients with respiratory disease. Several studies have demonstrated increased exhaled nitric oxide in patients with pulmonary disease, including asthma. In addition, exhaled nitric oxide may be an elegant tool for monitoring of environmental health effects of air pollution and the prevalence of atopy in epidemiological surveys. Recent literature about exhaled nitric oxide is presented in this article. Technical, physiological, and behavioral confounding factors of exhaled nitric oxide measurement are outlined.
Gamma-Ray Emission from the Broad-Line Radio Galaxy 3C 111

The broad-line radio galaxy 3C 111 has been suggested as the counterpart of the γ-ray source 3EG J0416+3650. While 3C 111 meets most of the criteria for a high-probability identification, like a bright flat-spectrum radio core and a blazar-like broadband SED, in the Third EGRET Catalog, the large positional offset of about 1.5° put 3C 111 outside the 99% probability region for 3EG J0416+3650, making this association questionable. We present a reanalysis of all available data for 3C 111 from the EGRET archives, resulting in probable detection of high-energy γ-ray emission above 1000 MeV from a position close to the nominal position of 3C 111, in two separate viewing periods (VPs), at a 3 σ level in each. A new source, GRO J0426+3747, appears to be present nearby, seen only in the >1000 MeV data. For >100 MeV, the data are in agreement with only one source (at the original catalog position) accounting for most of the EGRET-detected emission of 3EG J0416+3650. A follow-up Swift UVOT/XRT observation reveals one moderately bright X-ray source in the error box of 3EG J0416+3650, but because of the large EGRET position uncertainty, it is not certain that the X-ray and γ-ray sources are associated. A Swift observation of GRO J0426+3747 detected no X-ray source nearby.
Leaf respiration at different canopy positions in sweetgum (Liquidambar styraciflua) grown in ambient and elevated concentrations of carbon dioxide in the field.

Trees exposed to elevated CO2 partial pressure ([CO2]) generally show increased rates of photosynthesis and growth, but effects on leaf respiration are more variable. The causes of this variable response are unresolved. We grew 12-year-old sweetgum trees (Liquidambar styraciflua L.) in a Free-Air CO2 Enrichment (FACE) facility in ambient [CO2] (37/44 Pa daytime/nighttime) and elevated [CO2] (57/65 Pa daytime/nighttime) in native soil at Oak Ridge National Environmental Research Park. Nighttime respiration (R(N)) was measured on leaves in the upper and lower canopy in the second (1999) and third (2000) growing seasons of CO2 fumigation. Leaf respiration in the light (R(L)) was estimated by the technique of Brooks and Farquhar (1985) in the upper canopy during the third growing season. There were no significant short-term effects of elevated [CO2] on R(N) or long-term effects on R(N) or R(L), when expressed on an area, mass or nitrogen (N) basis. Upper-canopy leaves had 54% higher R(N) (area basis) than lower-canopy leaves, but this relationship was unaffected by CO2 growth treatment. In August 2000, R(L) was about 40% of R(N) in the upper canopy. Elevated [CO(2)] significantly increased the number of leaf mitochondria (62%), leaf mass per unit area (LMA; 9%), and leaf starch (31%) compared with leaves in ambient [CO(2)]. Upper-canopy leaves had a significantly higher number of mitochondria (73%), N (53%), LMA (38%), sugar (117%) and starch (23%) than lower-canopy leaves. Growth in elevated [CO2] did not affect the relationships (i.e., intercept and slope) between R(N) and the measured leaf characteristics. Although no factor explained more than 45% of the variation in R(N), leaf N and LMA were the best predictors for R(N). Therefore, the response of RN to CO2 treatment and canopy position was largely dependent on the magnitude of the effect of elevated [CO2] or canopy position on these characteristics. Because elevated [CO2] had little or no effect on N or LMA, there was no effect on R(N). Canopy position had large effects on these leaf characteristics, however, such that upper-canopy leaves exhibited higher R(N) than lower-canopy leaves. We conclude that elevated [CO2] does not directly impact leaf respiration in sweetgum and that barring changes in leaf nitrogen or leaf chemical composition, long-term effects of elevated [CO2] on respiration in this species will be minimal.
Spatial and temporal analysis of trends in extreme temperature indices in Iran over the period 1960–2014

The recent years have witnessed a rapid increase in frequency, severity, duration and geographical extent of extreme weather events. Having an area of 1 648 195 km2, Iran spans over a wide latitudinal range and enjoys a diverse terrain in terms of topography and elevation. The combination of this topographic complexity with the effects of extensive water bodies in the north and the south plays a major role in the distribution of temperature over this country. This study analysed the temporal trend of extreme temperature indices observed in 33 synoptic stations across Iran over the period 1960–2014, and then examined their relationship with elevation and latitude. The results showed a significant warming trend in extreme temperature indices of many stations, especially the indices that are based on daily minimum temperature. At low elevations, the trends of indices exhibited the features of a warming climate, but at higher elevations, these indices showed a mixture of positive and negative trends. Examining the relationship between the trends of indices and elevation showed that in the altitudinal band E1 [elevations lower than 23 m above sea level (ASL)], only the trend of growing season length is correlated with elevation; but in the altitudinal band E2 (elevations higher than 700 m ASL), elevation exhibited significant correlation with the trends of percentage of cool nights, frequency of frost days, diurnal temperature range, cold spell duration, percentage of warm nights and frequency of tropical nights. The analysis did not show any meaningful relationship between extreme temperature indices trends with latitude. Considering the high heterogeneity of the trends of indices and the limited number of stations with sufficient data, generalizing the results and predicting the wider trend patterns require further studies using a denser network of stations.
Multistream Recognition of Speech: Dealing With Unknown Unknowns

The paper discusses an approach for dealing with unexpected acoustic elements in speech. The approach is motivated by observations of human performance on such problems, which indicate the existence of multiple parallel processing streams in the human speech processing cognitive system, combined with the human ability to know when the correct information is being received. Some earlier relevant engineering approaches in multistream automatic recognition of speech (ASR) that aimed at processing of noisy speech and at dealing with unexpected out-of-vocabulary words are reviewed. The paper also reviews some currently active research in multistream ASR, focusing mainly on feedback-based techniques involving fusion of information between individual processing streams. The difference between the system behavior on its training data and during its operation is proposed as a substitute for the human ability of “knowing when knowing. ” Most recent results indicate 9% relative improvement in error rates in phoneme recognition of high signal-to-noise ratio speech and as high as 30% relative improvements in moderate noise.
Improving GPU Performance Through Resource Sharing

Graphics Processing Units (GPUs) consisting of Streaming Multiprocessors (SMs) achieve high throughput by running a large number of threads and context switching among them to hide execution latencies. The number of thread blocks, and hence the number of threads that can be launched on an SM, depends on the resource usage--e.g. number of registers, amount of shared memory--of the thread blocks. Since the allocation of threads to an SM is at the thread block granularity, some of the resources may not be used up completely and hence will be wasted. We propose an approach that shares the resources of SM to utilize the wasted resources by launching more thread blocks. We show the effectiveness of our approach for two resources: register sharing, and scratchpad (shared memory) sharing. We further propose optimizations to hide long execution latencies, thus reducing the number of stall cycles. We implemented our approach in GPGPU-Sim simulator and experimentally validated it on 19 applications from 4 different benchmark suites: GPGPU-Sim, Rodinia, CUDA-SDK, and Parboil. We observed that applications that underutilize register resource show a maximum improvement of 24% and an average improvement of 11% with register sharing. Similarly, the applications that underutilize scratchpad resource show a maximum improvement of 30% and an average improvement of 12.5% with scratchpad sharing. The remaining applications, which do not waste any resources, perform similar to the baseline approach.
Database Support for Probabilistic Attributes and Tuples

The inherent uncertainty of data present in numerous applications such as sensor databases, text annotations, and information retrieval motivate the need to handle imprecise data at the database level. Uncertainty can be at the attribute or tuple level and is present in both continuous and discrete data domains. This paper presents a model for handling arbitrary probabilistic uncertain data (both discrete and continuous) natively at the database level. Our approach leads to a natural and efficient representation for probabilistic data. We develop a model that is consistent with possible worlds semantics and closed under basic relational operators. This is the first model that accurately and efficiently handles both continuous and discrete uncertainty. The model is implemented in a real database system (PostgreSQL) and the effectiveness and efficiency of our approach is validated experimentally.