Miracle-dz/UniFAR-FTUs huggingface dataset:
Rearing a virulent common cuckoo is not extra costly for its only cavity-nesting host

Virulent brood parasites refrain from arduous parental care, often kill host progeny and inflict rearing costs upon their hosts. Quantifying the magnitude of such costs across the whole period of care (from incubation through to parasite fledgling independence) is essential for understanding the selection pressures on hosts to evolve antiparasitic defences. Despite the central importance of such costs for our understanding of coevolutionary dynamics, they have not yet been comprehensively quantified in any host of any avian brood parasite. We quantified parasite-rearing costs in common redstarts Phoenicurus phoenicurus raising either parasitic common cuckoo Cuculus canorus or their own chicks throughout the complete breeding cycle, and used multiple cost parameters for each breeding stage: incubation, brooding and feeding effort; length of parental/host care; parent/host body condition; and heterophil/lymphocyte ratio (stress-level indicator). Contrary to traditional assumptions, rearing the parasite per se was not associated with overall higher physiological or physical costs to hosts above the natural levels imposed by efforts to rear their own progeny. The low parasite-rearing costs imposed on hosts may, in part, explain the low levels of known host counter-defences in this unusually frequently parasitized cuckoo host.
Novel Dexamethasone Sodium Phosphate Treatment (DSP-Visulex) for Noninfectious Anterior Uveitis: A Randomized Phase I/II Clinical Trial

ABSTRACT Purpose: Frequent steroid drops represent a challenge in patient compliance. This study evaluated the safety and efficacy of 5 minute topical dexamethasone sodium phosphate-Visulex (DSP-Visulex) treatment regimen (two applications on the first week then weekly after) compared to daily prednisolone acetate 1% (PA) for noninfectious anterior uveitis. Materials and Methods: Forty-four patients were randomized to 8% DSP-Visulex with placebo eye drops (8% group, n = 14), 15% DSP-Visulex with placebo eye drops (15% group, n = 15), or Vehicle-Visulex with PA eye drops (PA group, n = 15). Patients received daily eye drops and Visulex treatments on days 1, 3, 8, and 15 with an optional treatment on day 22. Efficacy measures were change in anterior chamber cell (ACC) count from baseline and proportion of patients with zero ACC count at days 8, 15, and 29. Safety measures were adverse events (AEs), visual acuity, ocular symptoms, and intraocular pressure (IOP). Results: ACC resolution over time was similar among the three groups. The percentage of patients with clear ACC was 18%, 22%, and 15% on day 8; 27%, 56%, and 54% on day 15; and 90%, 88%, and 77% on day 29 for the 8%, 15%, and PA groups, respectively. The numbers of reported AEs were 10, 36, and 12 for the 8%, 15%, and PA groups, respectively. Ten patients among all groups experienced treatment-related AEs, which included headache, eye pain, corneal abrasion, conjunctival/corneal staining, conjunctivitis, visual acuity reduction, and keratitis all of which were resolved during the timeframe of patients’ participation in the study. IOP elevation was noted in the PA group throughout the study, whereas IOP elevation in the DSP-Visulex groups was observed at day 3 but not thereafter. Conclusions: The efficacy of the DSP-Visulex applications was comparable to the daily PA drops in the treatment of noninfectious anterior uveitis. Both 8% and 15% DSP-Visulex treatments were safe and well tolerated.
Spatio-temporal tumor heterogeneity in metastatic CRC tumors: a mutational-based approach

It is well known that activating mutations in the KRAS and NRAS genes are associated with poor response to anti-EGFR therapies in patients with metastatic colorectal cancer (mCRC). Approximately half of the patients with wild-type (WT) KRAS colorectal carcinoma do not respond to these therapies. This could be because the treatment decision is determined by the mutational profile of the primary tumor, regardless of the presence of small tumor subclones harboring RAS mutations in lymph nodes or liver metastases. We analyzed the mutational profile of the KRAS, NRAS, BRAF and PI3KCA genes using low-density microarray technology in samples of 26 paired primary tumors, 16 lymph nodes and 34 liver metastases from 26 untreated mCRC patients (n=76 samples). The most frequent mutations found in primary tumors were KRAS (15%) and PI3KCA (15%), followed by NRAS (8%) and BRAF (4%). The distribution of the mutations in the 16 lymph node metastases analyzed was as follows: 4 (25%) in KRAS gene, 3 (19%) in NRAS gene and 1 mutation each in PI3KCA and BRAF genes (6%). As expected, the most prevalent mutation in liver metastasis was in the KRAS gene (35%), followed by PI3KCA (9%) and BRAF (6%). Of the 26 cases studied, 15 (58%) displayed an overall concordance in the mutation status detected in the lymph node metastases and liver metastases compared with primary tumor, suggesting no clonal evolution. In contrast, the mutation profiles differed in the primary tumor and lymph node/metastases samples of the remaining 11 patients (48%), suggesting a spatial and temporal clonal evolution. We confirm the presence of different mutational profiles among primary tumors, lymph node metastases and liver metastases. Our results suggest the need to perform mutational analysis in all available tumor samples of patients before deciding to commence anti-EGFR treatment.
Efficient Learning of Restricted Boltzmann Machines Using Covariance estimates

Learning RBMs using standard algorithms such as CD(k) involves gradient descent on the negative log-likelihood. One of the terms in the gradient, which involves expectation w.r. t. the model distribution, is intractable and is obtained through an MCMC estimate. In this work we show that the Hessian of the log-likelihood can be written in terms of covariances of hidden and visible units and hence, all elements of the Hessian can also be estimated using the same MCMC samples with small extra computational costs. Since inverting the Hessian may be computationally expensive, we propose an algorithm that uses inverse of the diagonal approximation of the Hessian, instead. This essentially results in parameter-specific adaptive learning rates for the gradient descent process and improves the efficiency of learning RBMs compared to the standard methods. Specifically we show that using the inverse of diagonal approximation of Hessian in the stochastic DC (difference of convex functions) program approach results in very efficient learning of RBMs.
A Novel Approach for Detecting Road Based on Two-Stream Fusion Fully Convolutional Network

Road detection is one of the most basic tasks of autonomous driving systems. At present, researches on this issue mainly take two kinds of data as input, i.e., LIDAR point clouds and RGB images from cameras. To make best use of the advantages and bypass the disadvantages of these two kinds of data, we propose a novel network, namely two- stream fusion fully convolutional network (TSF-FCN), which can take advantage of both the accurate location information from LIDAR point clouds and rich appearance information from RGB images. One stream of this network is LIDAR stream which aggregates multi-scale contextual information from LIDAR point clouds. The other stream is RGB stream which is used for extracting features from RGB images. To fuse the two streams, the feature maps of RGB stream are converted to a bird-view representation to concatenate with that of LIDAR stream. In this way, the two kinds of data can complement each other for detecting road. To verify the efficacy of our TSF-FCN, experiments are carried on KITTI- ROAD benchmark and competitive performance is achieved compared with state-of-the-art methods.
An Exploratory Study of Search Based Training Data Selection for Cross Project Defect Prediction

Context: Search based approaches are gaining attention in cross project defect prediction (CPDP). The complexity of such approaches and existence of various design decisions are important issues to consider. Objective: We aim at investigating factors that can affect the performance of search based selection (SBS) approaches. We study a genetic instance selection approach (GIS) and present an evaluation of design options for search based CPDP. Method: Using an exploratory approach, data from different options of models are gathered and analyzed through ANOVA tests and effect sizes. Results: Both feature sets and validation dataset selection options show small or insignificant impacts on F-measure and precision, unlike the more affected false positive and true negative rates. Size of training data does not seem to be related to significant changes in F-measure and precision and high variability in performance are discouraging evidence for using larger datasets. Fitness function is one of the major factors that impact performance with much larger effect than the choice of validation dataset. Finally, while showing slight impacts, data label changes do not seem to be the top contributor to performance. Conclusions: We conclude that exploratory approaches can be effective for making design decisions in constructing search based CPDP models. Effect of individual tuned learners and their interaction with other affecting parameters and more in depth study of quality affecting factors guided by label changes are directions to investigate.
Treatment outcome in patients with breast conserving surgery after neoadjuvant therapy for breast carcinoma - a single institution experience.

PURPOSE The aim of this study was to analyze outcomes of breast conserving surgery (BCS) after neoadjuvant treatment (NAT) in comparison to radical mastectomy (RM) after NAT in terms of disease-free survival (DFS), overall survival (OS) and patients' satisfaction with the esthetic outcomes of surgery. METHODS This prospective study was conducted at the National Cancer Research Center of Serbia, Belgrade, from January 1st 2011 to December 31st 2015, on breast carcinoma patients receiving NAT. Treatment outcome was assessed by MDAPI (MD Anderson Prognostic Index). Female patients (n=52) with satisfactory clinical response to NAT and MDAPI scores 0 or 1 were included into the treatment group (NAT-BCS group). The control group (NAT-RM group) consisted of patients (n=52) with poorer clinical response and MDAPI scores 2 to 4. On check-ups, local or distant relapses were noted and both groups were asked to value their satisfaction with the esthetic outcomes of surgery using the Likert scale. RESULTS OS was 100% in both groups. DFS was 96.1% in NAT-BCS group and 100% in NAT-RM group. Local recurrences were observed in two patients from the age group ≥60 years, with initial disease stage IIIA and "clear" resection margins on frozen section study. Patients in the NAT-BCS group were more satisfied with the esthetic outcome of surgery than the control group. CONCLUSIONS BCS after NAT provides good esthetic outcome and is oncologically safe if adequate clinical response is achieved after NAT and if established criteria for patient selection are followed.
Seasonal Changes in the Physical Performance of Elite Youth Female Soccer Players.

Emmonds, S, Sawczuk, T, Scantlebury, S, Till, K, and Jones, B. Seasonal changes in the physical performance of elite youth female soccer players. J Strength Cond Res XX(X): 000-000, 2018-This study investigated the seasonal change in physical performance of 113 (Under 10: U10 [n = 20], U12 [n = 30], U14 [n = 31], and U16 [n = 32]) elite youth female soccer players. Players completed testing pre-, mid-, and post-season, including speed (10- and 30-m sprint), change of direction (CoD; 505 test), power (countermovement jump [CMJ]), strength (isometric midthigh pull), and aerobic capacity (Yo-Yo intermittent recovery test level 1 [YYIRL1]). A general linear model was used to evaluate the change in physical characteristics and the influence of covariates (baseline performance; change in maturity status) on each characteristic across the season. U10's speed and CoD performance decreased from pre-post season, whereas relative strength likely improved. U12's relative strength very likely improved; however, 10-m sprint performance decreased. Relative strength likely decreased, whereas 30-m sprint and CoD time very likely improved in U14's. U16's likely improved relative strength, CMJ, and 10-m sprint, and very likely improved 30-m sprint and CoD from pre-post season. U12-U16's improved YYIRL1 performance pre-post season. Strength and conditioning coaches working with U10-U12 players should look to develop speed, lower-body power, and CoD ability as part of structured strength and conditioning sessions as well as within warm-ups before pitch-based sessions. With U14-U16 players' manipulation of small-sided games combined with short-duration high-intensity running drills may provide an efficient training stimulus to develop the aerobic system while concurrently developing technical/tactical skills. Findings of this study provide a basis for the implementation of strategies to enhance the long-term athletic development of youth female soccer players.
Making Learning Personally Meaningful: A New Framework for Relevance Research

ABSTRACT Personal relevance goes by many names in the motivation literature, stemming from a number of theoretical frameworks. Currently these lines of research are being conducted in parallel with little synthesis across them, perhaps because there is no unifying definition of the relevance construct within which this research can be situated. In this paper we propose a new framework to synthesize existing research on relevance and provide a common platform for researchers to communicate and collaborate. In light of this new framework we review the role of relevance in three prominent theories in the motivation literature: the four-phase model of interest development, expectancy-value theory, and self-determination theory. We then explore eight relevance constructs commonly used in the literature and the educational interventions that derive from them. Finally, we offer a synthesis of these constructs and suggest some directions for future research.
ABIN2 Function Is Required To Suppress DSS-Induced Colitis by a Tpl2-Independent Mechanism

The A20-binding inhibitor of NF-κB 2 (ABIN2) interacts with Met1-linked ubiquitin chains and is an integral component of the tumor progression locus 2 (Tpl2) kinase complex. We generated a knock-in mouse expressing the ubiquitin-binding–defective mutant ABIN2[D310N]. The expression of Tpl2 and its activation by TLR agonists in macrophages or by IL-1β in fibroblasts from these mice was unimpaired, indicating that the interaction of ABIN2 with ubiquitin oligomers is not required for the stability or activation of Tpl2. The ABIN2[D310N] mice displayed intestinal inflammation and hypersensitivity to dextran sodium sulfate–induced colitis, an effect that was mediated by radiation-resistant cells rather than by hematopioetic cells. The IL-1β–dependent induction of cyclooxygenase 2 (COX2) and the secretion of PGE2 was reduced in mouse embryonic fibroblasts and intestinal myofibroblasts (IMFs) from ABIN2[D310N] mice. These observations are similar to those reported for the Tpl2 knockout (KO) mice (Roulis et al. 2014. Proc. Natl. Acad. Sci. USA 111: E4658–E4667), but the IL-1β–dependent production of COX2 and PGE2 in mouse embryonic fibroblasts or IMFs was unaffected by pharmacological inhibition of Tpl2 in wild-type mice. The expression of ABIN2 is decreased drastically in Tpl2 KO mice. These and other lines of evidence suggest that the hypersensitivity of Tpl2 KO mice to dextran sodium sulfate–induced colitis is not caused by the loss of Tpl2 catalytic activity but by the loss of ABIN2, which impairs COX2 and PGE2 production in IMFs by a Tpl2 kinase–independent pathway.
Batch Normalization Sampling

Deep Neural Networks (DNNs) thrive in recent years in which Batch Normalization (BN) plays an indispensable role. However, it has been observed that BN is costly due to the reduction operations. In this paper, we propose alleviating this problem through sampling only a small fraction of data for normalization at each iteration. Specifically, we model it as a statistical sampling problem and identify that by sampling less correlated data, we can largely reduce the requirement of the number of data for statistics estimation in BN, which directly simplifies the reduction operations. Based on this conclusion, we propose two sampling strategies, "Batch Sampling" (randomly select several samples from each batch) and "Feature Sampling" (randomly select a small patch from each feature map of all samples), that take both computational efficiency and sample correlation into consideration. Furthermore, we introduce an extremely simple variant of BN, termed as Virtual Dataset Normalization (VDN), that can normalize the activations well with few synthetical random samples. All the proposed methods are evaluated on various datasets and networks, where an overall training speedup by up to 20% on GPU is practically achieved without the support of any specialized libraries, and the loss on accuracy and convergence rate are negligible. Finally, we extend our work to the "micro-batch normalization" problem and yield comparable performance with existing approaches at the case of tiny batch size.
Comparative performance of IDEXX SDMA Test and the DLD SDMA ELISA for the measurement of SDMA in canine and feline serum

Kidney disease is common in companion animals, and traditionally diagnosed with serum creatinine concentration (sCr), blood urea nitrogen, and abnormal urinalysis findings. Symmetric dimethylarginine (SDMA) is a novel kidney biomarker that reflects glomerular filtration rate, increasing earlier than sCr with acute kidney injury and chronic kidney disease. This prospective study compared accuracy and precision of two commercial SDMA assays, the IDEXX SDMA Test and the DLD SDMA ELISA, relative to the established reference method, liquid chromatography/mass spectrometry (LC-MS). Thirty canine and 30 feline pooled serum samples were used to evaluate accuracy compared to LC-MS. Pooled canine samples with a low SDMA concentration and pooled feline samples with a high SDMA concentration were used to evaluate precision. Using a best fit linear model, the IDEXX SDMA Test resulted in a slope of 1.06 and an intercept of 0.34, with R2 = 0.99, and the DLD SDMA ELISA resulted in a slope of 0.37 and an intercept of 11.33, with R2 = 0.27, when compared to LC-MS. Estimated bias over a clinically relevant range for SDMA (10–45 μg/dL) was 1–2 μg/dL for the IDEXX SDMA Test, while DLD SDMA ELISA showed considerable bias, 5–8 μg/dL. Day-to-day precision analysis of the low SDMA concentration samples showed 7.7% total coefficient of variation (CV) for the IDEXX SDMA Test and 31.1% for the DLD SDMA ELISA. For the high SDMA concentration samples, total CV was 2.3% for the IDEXX SDMA Test and 28.2% for the DLD SDMA ELISA. In this study the IDEXX SDMA Test was more accurate and more precise in macroscopically normal serum than the DLD SDMA ELISA when compared to the reference method of LC-MS. The IDEXX SDMA Test is more suitable for clinical use in the diagnosis and monitoring of kidney disease in dogs and cats.
Lactobacillus plantarum 299v Reduces the Incidence of Clostridium difficile Infection in Nephrology and Transplantation Ward—Results of One Year Extended Study

Background:Lactobacillus plantarum 299v (LP299v) is a probiotic strain which influences on the intestinal bacterial flora. This is why, it has been introduced into clinical practice for the prevention and treatment of diarrheal disorders and alleviation of their symptoms in patients during antibiotic therapy. However, the use of probiotics in the prophylaxis of Clostridium difficile infections (CDI) in these patients is problematic. The aim of this clinical, retrospective, single-centre study was to analyse the incidence of CDI among patients hospitalized in the nephrology and transplantation ward in the period before, during and after stopping of LP299v prophylaxis. Methods: Among 5341 patients hospitalized in the nephrology and transplantation ward over a three year period, 34 patients with CDI were diagnosed and included in this analysis. From December 2013 to December 2014 all patients under antibiotic and immunosuppressive therapies received LP299v as a prophylaxis of CDI. The observation period consisted of three twelve-months periods: before, during LP299v use and after stopping of such method of CDI prevention. Results: A significant (p = 0.0003) reduction of CDI incidence during LP299v use (0.11%) was observed compared to two other periods, that is, before and after LP299v use (1.03% and 0.77%, respectively). Conclusions: Routine use of LP299v as a CDI prophylaxis may prevent CDI during antibiotics therapy in patients treated with immunosuppressive agents in nephrology and transplantation ward.
Expression of CD81 and CD117 in plasma cell myeloma and the relationship to prognosis

In this study, the immunophenotype was retrospectively analyzed in 131 patients who received initial treatment for plasma cell myeloma (PCM) and the relationships of CD81 and CD117 with the clinicopathologic characteristics and prognosis were further evaluated. The Kaplan and Meier method and Cox regression survival analysis model were used to determine whether CD117 and CD81 were factors affecting the overall survival (OS) and progression‐free survival (PFS) of PCM patients. CD117 and CD81 positivity was demonstrated in 35.88% and 40.46% of the 131 patients, respectively. Kaplan‐Meier analysis showed that CD117 and CD81 were potential predictors of a patient's prognosis. Specifically, CD117(+) patients had longer PFS (P = 0.033) and OS (P = 0.002), while CD81(+) patients had shorter PFS (P = 0.001) and OS (P = 0.002). CD117(+) and CD81(−) patients had the longest PFS [P = 0.0183 compared to the CD117(−)CD81(−)/CD117(+)CD81(+) group; P = 0.0007 compared to the CD117(−)CD81(+) group] and the longest OS [P = 0.0331 compared to the CD117(−)CD81(−)/CD117(+)CD81(+) group; P = 0.0005 compared to the CD117(−)CD81(+) group]. Our results show that CD81 is an independent factor affecting the OS and PFS of PCM patients, and CD117 is an independent factor affecting the OS of PCM patients. CD117‐positive and CD81‐negative patients with PCM have a better prognosis.
Interlaboratory comparison of the TransFix®/EDTA Vacuum Blood Collection tube with the 5 mL Cyto‐Chex® BCT

An interlaboratory study was performed to compare the performance of the 3 mL TransFix®/EDTA Vacuum Blood Collection Tube (TVT), with the 5 mL Cyto‐Chex® BCT tube (BCT). Both devices are intended for collection and storage of whole blood specimens for immunophenotyping of leukocytes by flow cytometry for up to 14 days.