Miracle-dz/UniFAR-FTUs huggingface dataset:
Erythrocyte responses in low-shear-rate flows: effects of non-biconcave stress-free state in the cytoskeleton

Abstract Inspired by the recent experiment on erythrocytes (red blood cells, RBCs) in weak shear flows by Dupire et al. (Proc. Natl Acad. Sci. USA, vol. 109, 2012, pp. 20808–20813), we conduct a numerical investigation to study the dynamics of RBCs in low-shear-rate flows by applying a multiscale fluid–structure interaction model. By employing a spheroidal stress-free state in the cytoskeleton, we are able to numerically predict an important feature, namely that the cell maintains its biconcave shape during tank-treading motions. Furthermore, we numerically confirm the hypothesis that, as the stress-free state approaches a sphere, the threshold shear rates corresponding to the establishment of tank treading decrease. By comparing with the experimental measurements, our study suggests that the stress-free state of RBCs is a spheroid that is close to a sphere, rather than the biconcave shape applied in existing models (the implication is that the RBC skeleton is pre-stressed in its natural biconcave state). It also suggests that the response of RBCs in low-shear-rate flows may provide a measure to quantitatively determine the distribution of shear stress in the RBC cytoskeleton in the natural state.
The dribbling agility test as a potential tool for evaluating the dribbling skill in young soccer players

ABSTRACT The present study examined the construct validity and reliability of a new dribbling agility test (DAT) that incorporates reactive agility and multiple change of direction. To check its’ validity, (a) DAT was performed by four groups (under 10, under 12, under 14 and under 16 yrs) of young soccer players (n = 125 in each group) and (b) a regression analysis was conducted to define the best DAT predictors. The reliability of DAT was assessed with repeated measurements. This test can differentiate the dribbling skill between groups (p < 0.01). Furthermore, 68% of the observed variance in DAT was explained by zigzag dribbling test, Illinois agility test, reaction time and running speed. The test-retest reliability was high in all groups (ICC = 0.77 – 0.90, p < 0.01). It was concluded that DAT can be a potential tool to evaluate the dribbling performance in young soccer players.
Coalitions Matter: Citizenship, Women, and Quota Adoption in Africa

We provide new theory and evidence of the role of domestic women’s coalitions in the adoption of gender quotas. Previous research has shown the importance of women’s movements to policy change. We show that specific types of mobilization, often multiethnic in character, are a more precise way of describing these influences. Using a new dataset of coalitions in 50 countries in Africa (1989–2014), we first examine where coalitions are likely to emerge. Controlling for factors that correlate with their formation, we find that when domestic women’s organizations form a coalition for quotas, governments are more likely to adopt them and do so more quickly. This correlation holds when controlling for international aid, involvement of international women’s movements, and whether countries recently emerged out of major armed conflict, complementing recent scholarship that highlights global influences. A comparative case study of the adoption of a gender quota in Senegal and non-adoption in Benin helps illustrate the nuances of the theory.
Transfer and Expression of ALS Inhibitor Resistance from Palmer Amaranth (Amaranthus palmeri) to an A. spinosus × A. palmeri Hybrid

Abstract Transfer of herbicide resistance among closely related weed species is a topic of growing concern. A spiny amaranth × Palmer amaranth hybrid was confirmed resistant to several acetolactate synthase (ALS) inhibitors including imazethapyr, nicosulfuron, pyrithiobac, and trifloxysulfuron. Enzyme assays indicated that the ALS enzyme was insensitive to pyrithiobac and sequencing revealed the presence of a known resistance conferring point mutation, Trp574Leu. Alignment of the ALS gene for Palmer amaranth, spiny amaranth, and putative hybrids revealed the presence of Palmer amaranth ALS sequence in the hybrids rather than spiny amaranth ALS sequences. In addition, sequence upstream of the ALS in the hybrids matched Palmer amaranth and not spiny amaranth. The potential for transfer of ALS inhibitor resistance by hybridization has been demonstrated in the greenhouse and in field experiments. This is the first report of gene transfer for ALS inhibitor resistance documented to occur in the field without artificial/human intervention. These results highlight the need to control related species in both field and surrounding noncrop areas to avoid interspecific transfer of resistance genes. Nomenclature: Imazethapyr, nicosulfuron, pyrithiobac, trifloxysulfuron, Palmer amaranth Amaranthus palmeri S. Wats, spiny amaranth (Amaranthus spinosus L.).
Test-Retest Reliability and Practice Effects of a Computerized Neuropsychological Battery: A Solution-Oriented Approach

This study examined test-retest reliabilities and (predictors of) practice effects of the widely used computerized neuropsychological battery CNS Vital Signs. The sample consisted of 158 Dutch healthy adults. At 3 and 12 months follow-up, 131 and 77 participants were retested. Results revealed low to high test–retest reliability coefficients for CNS VS’ test and domain scores. Participants scored significantly higher on the domains of Cognitive Flexibility, Processing Speed, and Reaction Time at the 3-month retest. No significant differences in performance were found over the second interval. Age, education, and retest-interval were not significantly associated with practice effects. These results highlight the need for methods that evaluate performance over time while accounting for imperfect test-retest reliabilities and practice effects. We provided RCI-formulae for determining reliable change, which may be possible solution for future work facing the methodological issues of retesting.
Palladium-catalyzed cross-coupling reactions of paramagnetic vinyl bromides and paramagnetic boronic acids

Suzuki reactions are utilized for the synthesis of hetero- bifunctional cross-linking reagents (thiol- or aminospecific and photoactivatable), polyaromatics (such as phenanthrene) and het- erocycles (such as coumarin and quinoline), anellated nitroxides and paramagnetic, biologically active molecules (such as cis-stil- bene and nicotinamide). Furthermore, the synthesis of new vinyl and allyl boronic acid esters is also reported.
Self-focusing and filamentation of optical vortex beams: spatio-temporal analysis

We report numerical simulations supported by experimental observations of self-focusing, fillamentation, and supercontinuum generation by an optical vortex beam in a Kerr nonlinear medium in the regime of dominating nonlinearity. Despite the strong self-focusing resulting in multiple filaments ordered along the vortex ring the optical vortex remains well preserved at the exit of the nonlinear medium and in the far-field. The presented quasi-(3+1)- dimensional numerical simulations under azimuthal initial vortex ring perturbations confirm qualitatively the experimentally observed survival of the optical vortex in the course of the white light generation.
P2RX7 Purinoceptor as a Therapeutic Target—The Second Coming?

The P2RX7 receptor is a unique member of a family of extracellular ATP (eATP)-gated ion channels expressed in immune cells, where its activation triggers the inflammatory cascade. Therefore, P2RX7 has been long investigated as a target in the treatment of infectious and inflammatory diseases. Subsequently, P2RX7 signaling has been documented in other physiological and pathological processes including pain, CNS and psychiatric disorders and cancer. As a result, a range of P2RX7 antagonists have been developed and trialed. Interestingly, the recent crystallization of mammalian and chicken receptors revealed that most widely-used antagonists may bind a unique allosteric site. The availability of crystal structures allows rational design of improved antagonists and modeling of binding sites of the known or presumed inhibitors. However, several unanswered questions limit the cogent development of P2RX7 therapies. Firstly, this receptor functions as an ion channel, but its chronic stimulation by high eATP causes opening of the non-selective large pore (LP), which can trigger cell death. Not only the molecular mechanism of LP opening is still not fully understood but its function(s) are also unclear. Furthermore, how can tumor cells take advantage of P2RX7 for growth and spread and yet survive overexpression of potentially cytotoxic LP in the eATP-rich environment? The recent discovery of the feedback loop, wherein the LP-evoked release of active MMP-2 triggers the receptor cleavage, provided one explanation. Another mechanism might be that of cancer cells expressing a structurally altered P2RX7 receptor, devoid of the LP function. Exploiting such mechanisms should lead to the development of new, less toxic anticancer treatments. Notably, targeted inhibition of P2RX7 is crucial as its global blockade reduces the immune and inflammatory responses, which have important anti-tumor effects in some types of malignancies. Therefore, another novel approach is the synthesis of tissue/cell specific P2RX7 antagonists. Progress has been aided by the development of p2rx7 knockout mice and new conditional knock-in and knock-out models are being created. In this review, we seek to summarize the recent advances in our understanding of molecular mechanisms of receptor activation and inhibition, which cause its re-emergence as an important therapeutic target. We also highlight the key difficulties affecting this development.
Bayes Certificateless Signcryption Based Secured Data Integrity for Cloud Service Provisioning

Large amount of sensitive data is shared to other cloud users in cloud computing environment. To maintain data integrity, security, confidentiality, the data owners encrypt their data before transmission. However, the existing encryption techniques do not provide more security and data integrity rate. In order to overcome such limitations, Bayes Certificateless Signcryption Based Data Integrity (BCS-DI) technique is proposed. It is designed with the objective of improving the security of cloud service provisioning with higher data integrity rate. At first, the cloud users send data request to cloud server. Then, the cloud server analyzes the user request and provides required data. Before transmitting the data to corresponding users, Certificateless Signcryption is used to encrypt the user required data to be transmitted over a cloud network with sender private key which resulting in cipher text. This cipher text is send to the appropriate cloud user in cloud computing environment. Finally, digital signature verification process is carried out at the receiver side to access the original data by using Bayes theorem. The authorized cloud receiver can only obtain the original data when the signature of both sender and receiver is valid. This helps for BCS-DI technique to improve the security and data integrity rate. This technique conducts the experimental works on the parameters such as data security rate, execution time, memory utilization and data integrity rate. The experimental result shows that the BCS-DI technique is able to improve the data security rate and integrity rate of cloud service provisioning.
Gene prioritization using Bayesian matrix factorization with genomic and phenotypic side information

Motivation Most gene prioritization methods model each disease or phenotype individually, but this fails to capture patterns common to several diseases or phenotypes. To overcome this limitation, we formulate the gene prioritization task as the factorization of a sparsely filled gene‐phenotype matrix, where the objective is to predict the unknown matrix entries. To deliver more accurate gene‐phenotype matrix completion, we extend classical Bayesian matrix factorization to work with multiple side information sources. The availability of side information allows us to make non‐trivial predictions for genes for which no previous disease association is known. Results Our gene prioritization method can innovatively not only integrate data sources describing genes, but also data sources describing Human Phenotype Ontology terms. Experimental results on our benchmarks show that our proposed model can effectively improve accuracy over the well‐established gene prioritization method, Endeavour. In particular, our proposed method offers promising results on diseases of the nervous system; diseases of the eye and adnexa; endocrine, nutritional and metabolic diseases; and congenital malformations, deformations and chromosomal abnormalities, when compared to Endeavour. Availability and implementation The Bayesian data fusion method is implemented as a Python/C++ package: https://github.com/jaak‐s/macau. It is also available as a Julia package: https://github.com/jaak‐s/BayesianDataFusion.jl. All data and benchmarks generated or analyzed during this study can be downloaded at https://owncloud.esat. kuleuven.be/index.php/s/UGb89WfkZwMYoTn.
PrimAlign: PageRank-inspired Markovian alignment for large biological networks

Motivation Cross‐species analysis of large‐scale protein‐protein interaction (PPI) networks has played a significant role in understanding the principles deriving evolution of cellular organizations and functions. Recently, network alignment algorithms have been proposed to predict conserved interactions and functions of proteins. These approaches are based on the notion that orthologous proteins across species are sequentially similar and that topology of PPIs between orthologs is often conserved. However, high accuracy and scalability of network alignment are still a challenge. Results We propose a novel pairwise global network alignment algorithm, called PrimAlign, which is modeled as a Markov chain and iteratively transited until convergence. The proposed algorithm also incorporates the principles of PageRank. This approach is evaluated on tasks with human, yeast and fruit fly PPI networks. The experimental results demonstrate that PrimAlign outperforms several prevalent methods with statistically significant differences in multiple evaluation measures. PrimAlign, which is multi‐platform, achieves superior performance in runtime with its linear asymptotic time complexity. Further evaluation is done with synthetic networks and results suggest that popular topological measures do not reflect real precision of alignments. Availability and implementation The source code is available at http://web.ecs. baylor.edu/faculty/cho/PrimAlign.
Training for translation between disciplines: a philosophy for life and data sciences curricula

Motivation Our society has become data‐rich to the extent that research in many areas has become impossible without computational approaches. Educational programmes seem to be lagging behind this development. At the same time, there is a growing need not only for strong data science skills, but foremost for the ability to both translate between tools and methods on the one hand, and application and problems on the other. Results Here we present our experiences with shaping and running a masters' programme in bioinformatics and systems biology in Amsterdam. From this, we have developed a comprehensive philosophy on how translation in training may be achieved in a dynamic and multidisciplinary research area, which is described here. We furthermore describe two requirements that enable translation, which we have found to be crucial: sufficient depth and focus on multidisciplinary topic areas, coupled with a balanced breadth from adjacent disciplines. Finally, we present concrete suggestions on how this may be implemented in practice, which may be relevant for the effectiveness of life science and data science curricula in general, and of particular interest to those who are in the process of setting up such curricula.
Accuracy of Post-Void Residual Urine Volume Measurement Using an Ultrasound Bladder Scanner among Postoperative Radical Hysterectomy Patients.

Background Postoperative urinary retention occurs in 17 to 42% of Radical hysterectomy (RH) cases. The gold standard assessment of post-void residual urine volume (PVR) is bladder catheterization. The use of the 3D portable ultrasound device (VerathonBladderScan BVI 9400) to evaluate PVR is quick, safe, non-invasive, painless, and comfortable for patients as well as being easy to use. Objective To compare the accuracy of ultrasound bladder scanner with that of urethral catheterization in the assessment of post-void residual urine volume (PVR). Material and Method This was a prospective study. After removal of Foley’s catheter in postoperative radical hysterectomy(RH) patients, the voiding care schedule consisted of voids after six hours or earlier if the patient had the urge. Promptly after voiding, PVR was measured using the BladderScan (Scan volume). Immediately after the procedure, urethral catheterization was performed to obtain the actual PVR (Catheter volume). The process was repeated in subsequent voids, and correlations between scan volume and catheter volume were analyzed. Results Seventy patients (140 measurements) were included. A high correlation was found between the scan volume and the catheter volume (r = 0.89, p<0.001). A 91.0% specificity and 93.1% negative predictive value(NPV) were obtained using the scan volume in predicting a catheter volume of <100 ml. The difference in measurements between the two methods was not related to age, body mass index, parity, co-existing illness, type of surgical incision or duration of indwelling catheter. When catheter volume >100 ml was the cutoff for determining the need for re-catheterization, the scan volume returned 90.0% accuracy. Repetition of ultrasound scan in patients who had a first scan volume of <100 ml yielded a 97.2% specificity and 100% NPV in predicting catheter volume of <100 ml. Conclusion The Bladder Scan provides good correlation together with high rates of specificity and NPV, and it could be an alternative modality to catheterization for the measurement of PVR in postoperative RH patients.
Convex Geometries are Extremal for the Generalized Sauer-Shelah Bound

The Sauer-Shelah lemma provides an exact upper bound on the size of set families with bounded Vapnik-Chervonekis dimension. When applied to lattices represented as closure systems, this lemma outlines a class of extremal lattices obtaining this bound. Here we show that the Sauer-Shelah bound can be easily generalized to arbitrary antichains, and extremal objects for this generalized bound are exactly convex geometries. We also show that the problem of classification of antichains admitting such extremal objects is NP-complete.
An Analysis of Women's Fertility and Labor Supply: Implications for Family Policies

: A drastic decline in fertility rates in Korea is accelerating the unprecedentedly rapid population ageing. This phenomenon calls into question what role the economic forces play in the decisions and which public policies can be eﬀective. As population ageing induces a shortage of labor force that sustain the economic growth, this paper notes that stimulating women’s labor supply as well as encouraging fertility is a very important policy goal in an ageing society. Having this in mind, I investigate the eﬀectiveness of family policies that are frequently used in developed countries. For this purpose, I ﬁrst analyze the dynamic decisions of fertility and labor supply in a lifecycle framework, where time costs associated with children, time and goods investment in children, and uncertainties in earnings are important determinants of women’s decisions. Based on the model, I then conduct policy experiments which evaluate the eﬀects of policies including child allowances, conditional childcare subsidies, pronatal income tax, and maternal leaves. The ﬁndings show that providing beneﬁts conditional on or through labor market activities are more eﬀective than the provision of unconditional transfer in encouraging fertility without reducing labor supply of women.
Avian thermoregulation in the heat: is evaporative cooling more economical in nocturnal birds?

ABSTRACT Evaporative cooling is a prerequisite for avian occupancy of hot, arid environments, and is the only avenue of heat dissipation when air temperatures (Ta) exceed body temperature (Tb). Whereas diurnal birds can potentially rehydrate throughout the day, nocturnal species typically forgo drinking between sunrise and sunset. We hypothesized that nocturnal birds have evolved reduced rates of evaporative water loss (EWL) and more economical evaporative cooling mechanisms compared with diurnal species, permitting nocturnal species to tolerate extended periods of intense heat without becoming lethally dehydrated. We used phylogenetically informed regressions to compare EWL and evaporative cooling efficiency [ratio of evaporative heat loss (EHL) and metabolic heat production (MHP); EHL/MHP] among nocturnal and diurnal birds at high Ta. We analyzed variation in three response variables: (1) slope of EWL at Ta between 40 and 46°C, (2) EWL at Ta=46°C and (3) EHL/MHP at Ta=46°C. Nocturnality emerged as a weak, negative predictor, with nocturnal species having slightly shallower slopes and reduced EWL compared with diurnal species of similar mass. In contrast, nocturnal activity was positively correlated with EHL/MHP, indicating a greater capacity for evaporative cooling in nocturnal birds. However, our analysis also revealed conspicuous differences among nocturnal taxa. Caprimulgids and Australian owlet-nightjars had shallower slopes and reduced EWL compared with similarly sized diurnal species, whereas owls had EWL rates comparable to those of diurnal species. Consequently, our results did not unequivocally demonstrate more economical cooling among nocturnal birds. Owls predominately select refugia with cooler microclimates, but the more frequent and intense heat waves forecast for the 21st century may increase microclimate temperatures and the necessity for active heat dissipation, potentially increasing owls' vulnerability to dehydration and hyperthermia. Summary: Caprimulgids and Australian owlet-nightjars displayed allometrically lower water losses compared with diurnal birds, whereas owls exhibited water losses comparable to those of similarly sized diurnal birds.
A randomized controlled trial of a supportive expressive group intervention for women with a family history of breast cancer

Women with a family history of breast cancer (BC) often overestimate their BC risk. Heightened psychological distress may interfere with risk comprehension and screening adherence. The primary purpose of this study was to test the efficacy of a 12‐week manual‐based supportive‐expressive (SE) group intervention for this population.