Miracle-dz/UniFAR-FTUs huggingface dataset:
Abnormal Calcium Handling in Muscular Dystrophy

Duchenne muscular dystrophy, primarily caused by a deficiency in the membrane cytoskeletal protein dystrophin, is the most frequent neuromuscular disorder in humans and is characterized by progressive muscle weakness and wasting. This review outlines pathophysiological mechanisms of abnormal calcium handling by the sarcolemma, sarcoplasmic reticulum and mitochondria that may contribute to muscle fibre destruction. Dystrophindeficient skeletal muscle membranes succumb to exercise-induced membrane ruptures more frequently than those of normal fibres. These transient micro-ruptures allow for the insertion of calcium leak channels into the sarcolemma during the natural processes of cell membrane resealing. Ion leak channels give rise to localized calcium elevations, contributing to a cycle of enhanced protease activity and leak channel activation. Within the sarcoplasmic reticulum, loss of the calsequestrin-like proteins may contribute to decreased luminal calcium buffering. This might indirectly amplify elevated free cytosolic calcium concentrations. Mitochondria proximal to ryanodine receptor calcium release channel complexes, although thought to buffer channel leakiness, may give rise to an increase in proapoptotic signals, ultimately giving rise to muscle cell death. Here, we summarise the potential effects of abnormal calcium homeostasis on fibre degeneration in dystrophic skeletal muscle.
Penalized Sieve Estimation and Inference of Semi-Nonparametric Dynamic Models: A Selective Review

In this selective review, we first provide some empirical examples that motivate the usefulness of semi-nonparametric techniques in modelling economic and financial time series. We describe popular classes of semi-nonparametric dynamic models and some temporal dependence properties. We then present penalized sieve extremum (PSE) estimation as a general method for semi-nonparametric models with cross-sectional, panel, time series, or spatial data. The method is especially powerful in estimating difficult ill-posed inverse problems such as semi-nonparametric mixtures or conditional moment restrictions. We review recent advances on inference and large sample properties of the PSE estimators, which include (1) consistency and convergence rates of the PSE estimator of the nonparametric part; (2) limiting distributions of plug-in PSE estimators of functionals that are either smooth (i.e., root-n estimable) or non-smooth (i.e., slower than root-n estimable); (3) simple criterion-based inference for plug-in PSE estimation of smooth or non-smooth functionals; and (4) root-n asymptotic normality of semiparametric two-step estimators and their consistent variance estimators. Examples from dynamic asset pricing, nonlinear spatial VAR, semiparametric GARCH, and copula-based multivariate financial models are used to illustrate the general results.
A higher-order method for finding vortex core lines

This paper presents a novel method to extract vortical structures from 3D CFD (computational fluid dynamics) vector fields automatically. It discusses the underlying theory and some aspects of the implementation. Making use of higher-order derivatives, the method is able to locate bent vortices. In order to structure the recognition procedure, we distinguish locating the core line from calculating attributes of strength and quality. Results are presented on several flow fields from the field of turbomachinery.
The regionalization of radical cystectomy to specific medical centers.

PURPOSE Regionalization of high risk surgical procedures to larger teaching hospitals has been suggested as a means to improve the quality of care. We established a novel framework for characterizing regionalization, implemented it to determine the extent to which regionalization of radical cystectomy has occurred and delineated whether specific patient characteristics are associated with this phenomenon. MATERIALS AND METHODS We used the Nationwide Inpatient Sample to identify 22,088 patients who underwent radical cystectomy for bladder cancer from 1988 to 2000. Regionalization was assessed using 5 structural hospital measures, including teaching status, urban location, discharge volume, cystectomy volume and bed capacity. Adjusted models were developed to identify the significance of temporal trends and assess the association of demographic factors with structural qualities. RESULTS Compared with 1988 to 1990 subjects were more likely to undergo cystectomy at teaching hospitals (OR 1.8), high cystectomy volume hospitals (OR 1.2), high discharge volume hospitals (OR 1.7) and large bed capacity medical centers (OR 1.4) in 1998 to 2000. The concentration of cystectomy to urban medical centers during the study years was 90% to 92%. The proportion of subjects undergoing partial cystectomy decreased from 23.9% to 16.6% as regionalization occurred. Older subjects were less likely to be treated at these regionalized centers. CONCLUSIONS Without broad legislation from health care payers radical cystectomy has increasingly regionalized to specific medical centers. Despite this regionalization disparities in its use exist among specific, vulnerable patients. Addressing this may facilitate further concentration of this procedure.
Efficient multimatch packet classification and lookup with TCAM

Today's packet classification systems are designed to provide the highest-priority matching result, such as the longest prefix match, even if a packet matches multiple classification rules. However, new network applications demanding multimatch classification - that is, requiring all matching results instead of only the highest-priority match - are emerging. Ternary content-addressable memory is becoming a common extension to network processors, and its capability and speed make it attractive for high-speed networks. The proposed TCAM-based scheme produces multimatch classification results with about 10 times fewer memory lookups than a pure software approach. In addition, their scheme for removing negation in rule sets saves up to 95 percent of the TCAM space used by a straightforward implementation.
Can Music Preference Indicate Mental Health Status in Young People?

Objective: In the aftermath of the double suicide of two teenage girls in 2007, the media linked the themes of ‘emo’ music and the girls’ mental state. But it is not just emo music that has been the subject of scrutiny by the media. Rap music, country, and heavy metal have also been blamed for antisocial behaviours including violence, theft, promiscuity and drug use. It remains an important research and clinical question as to whether music contributes to the acting out of behaviours described in the music lyrics or whether the preferred music represents the already existing behavioural tendencies in the subject. This paper surveys and discusses the relevant literature on music preference and adolescent music listening behaviours, and their links with adolescent mental health. Conclusion: Studies have found a relationship between various genres of music and antisocial behaviours, vulnerability to suicide, and drug use. However, studies reject that music is a causal factor and suggest that music preference is more indicative of emotional vulnerability. A limited number of studies have found correlations between music preference and mental health status. More research is needed to determine whether music preferences of those with diagnosed mental health issues differ substantially from the general adolescent population.
Rigidity of the Economic Right? Menu-Independent and Menu-Dependent Influences of Psychological Dispositions on Political Attitudes

The rigidity of the right model posits that psychological needs for security and certainty (NSC) attract people to a broad right-wing ideology that includes both sociocultural and economic political attitudes. We review evidence that NSC characteristics do not consistently predict economically right-wing preferences and propose the Menu-Independent and -Dependent Influence (MIDI) model as an alternative account of disposition-politics relations. In this model, NSC naturally attracts people to socioculturally conservative attitudes, but its effects on economic attitudes are the net outcome of potentially competing dispositional and discursive influences. We review evidence in support of the MIDI model and discuss its implications for understanding the interplay of background characteristics, social context, and political conflict.
Breakdown of the Robustness Property of Lotka's Law: The Case of Adjusted Counts for Multiauthorship Attribution

It is generally agreed that the best way to handle multiauthored papers is to assign credit proportionally. Thus, if a paper is written by two authors, each would get half credit. Three authors would get a third each, and so on. This has been proposed by Lindsey (1980); see Egghe and Rousseau (1990, 111.2.4.2) for more details. This method of counting is called “adjusted counts” or “fractional counts. ” Other possible methods are “normal counts,” which gives full credit to all contributors and “straight counts,” which takes no account of multiple authorship and allocates the paper to the first author. However, very few, if any, papers have been published which study the authorship distribution when using adjusted counts. Further, Bookstein (1990) has shown that under certain hypotheses, it does not matter which method one uses: if one finds a Lotka distribution for one method of counting, one also finds a Lotka distribution for any other method. This result is one aspect of the so-called robustness property of Lotka’s law (see also Bookstein, 1977, 1991). More precisely, Bookstein (1990) writes:
Dual effects of constitutively active androgen receptor and full-length androgen receptor for N-cadherin regulation in prostate cancer

Constitutively active androgen receptor (AR) variants have been involved in the expression of mesenchymal markers such as N-cadherin in prostate cancer (PCa). However, the underlying molecular mechanisms remain elusive. It remains unclear, whether N-cadherin gene (CDH2) is a direct transcriptional target of AR variants or whether the observed upregulation is due to indirect effects through additional regulatory factors. Moreover, the specific contribution of full-length AR and AR variants in N-cadherin regulation in PCa has never been explored deeply. To investigate this, we artificially mimicked the co-expression of AR variants together with a full-length AR and performed miRNA-seq, RNA-seq and ChIP assays. Our results were in favor of a direct AR variants action on CDH2. Our data also revealed a distinctive mode of action between full-length AR and AR variants to regulate N-cadherin expression. Both wild type AR and AR variants could interact with a regulatory element in intron 1 of CDH2. However, a higher histone H4 acetylation in this genomic region was only observed with AR variants. This suggests that full-length AR may play an occluding function to impede CDH2 upregulation. Our data further highlighted a negative effect of AR variants on the expression of the endogenous full-length AR in LNCaP. These differences in the mode of action of AR variants and full-length AR for the control of one key gene for prostate cancer progression could be worth considering for targeting AR variants in PCa.
Biofilm in vitro; Biofilm in vivo Helicobacter pylori: A chameleon-like approach to life

Helicobacter pylori (H. pylori) is widely adaptable for colonization in human stomachs in more than half of the world’s population. The microorganism is characterized by an unusual capability of arranging itself in both genotypic and phenotypic ways. Stressing conditions, including antimicrobial agents in sub-inhibitory concentrations, facilitate entering the viable but nonculturable state in which bacterial cells acquire the coccoid form. This morphotype represents an important strategy for bacterial survival in unsuitable conditions and also allows escape from the immune system. H. pylori is capable of forming biofilm outside and inside the host. For the bacterial population, the sessile growth mode represents an ideal environment for gene rearrangement, as it allows the acquiring of important tools aimed to improve bacterial “fitness” and species preservation. Biofilm formation in H. pylori in the human host also leads to recalcitrance to antibiotic treatment, thus hampering eradication. These lifestyle changes of H. pylori allow for a “safe haven” for its survival and persistence according to different ecologi-cal niches, and strongly emphasize the need for careful H. pylori surveillance to improve management of the infection. and tends to The present review is focused on the general phenomenon of the fickleness in H. pylori and analyses the significance and role of this “chameleon-like” approach to life in the persistence of this fastidious bacterium outside and inside the host.
Review of modelling crack initiation and propagation in flexible pavements using the finite element method

Abstract Cracking is a major failure mechanism that directly affects the functionality and performance of flexible pavements. The objective of this study is to present the state of knowledge on the use of finite element method (FEM) including cohesive zone model (CZM) to simulate cracking failure mechanisms in flexible pavements under field conditions. Based on this review, a knowledge base is established on how FEM can be effectively applied to predict pavement performance against cracking failure mechanisms. Two main approaches are presented in this study. In the first approach, focused finite element (FE) meshes are used to simulate the crack initiation and propagation phases. Focused meshes allow for estimating the J-integral and the stress intensity factor (SIF) through different contour lines. Since the SIF is a measure of the stress and strain environment around the crack tip (a greater SIF indicates a faster rate of propagation), the rate of crack propagation per cycle can be estimated based on empirical equations such as Paris’ Law. In the second approach, the propagation of damage is simulated using FE and CZM. This approach allows one to study the loading mechanisms responsible for progressing cracking damage in the pavement structure. In summary, both approaches have merits in modelling cracking in flexible pavements. While focused meshes may be used to predict the number of cycles for crack propagation, CZM may be used to study the controlling stresses and mechanisms responsible for crack propagation.
A Comprehensive Analysis of Polyhedral Lift-and-Project Methods

We consider lift-and-project methods for combinatorial optimization problems and focus mostly on those lift-and-project methods which generate polyhedral relaxations of the convex hull of integer solutions. We introduce many new variants of Sherali--Adams and Bienstock--Zuckerberg operators. These new operators fill the spectrum of polyhedral lift-and-project operators in a way which makes all of them more transparent, easier to relate to each other, and easier to analyze. We provide new techniques to analyze the worst-case performances as well as relative strengths of these operators in a unified way. In particular, using the new techniques and a result of Mathieu and Sinclair from 2009, we prove that the polyhedral Bienstock--Zuckerberg operator requires at least $\sqrt{2n}- \frac{3}{2}$ iterations to compute the matching polytope of the $(2n+1)$-clique. We further prove that the operator requires approximately $\frac{n}{2}$ iterations to reach the stable set polytope of the $n$-clique, if we start with the fractional stable set polytope. Lastly, we show that some of the worst-case instances for the positive semidefinite Lov\'asz--Schrijver lift-and-project operator are also bad instances for the strongest variants of the Sherali--Adams operator with positive semidefinite strengthenings, and discuss some consequences for integrality gaps of convex relaxations.
On synchronous robotic networks Part II: Time complexity of rendezvous and deployment algorithms

This paper analyzes a number of basic coordination algorithms running on synchronous robotic networks. We provide upper and lower bounds on the time complexity of the move-toward average and circumcenter laws, both achieving rendezvous, and of the centroid law, achieving deployment over a region of interest. The results are derived via novel analysis methods, including a set of results on the convergence rates of linear dynamical systems defined by tridiagonal Toeplitz and circulant matrices.
Recent Evolution in Rattus norvegicus Is Shaped by Declining Effective Population Size

The brown rat, Rattus norvegicus, is both a notorious pest and a frequently used model in biomedical research. By analysing genome sequences of 12 wild-caught brown rats from their ancestral range in NE China, along with the sequence of a black rat, R. rattus, we investigate the selective and demographic forces shaping variation in the genome. We estimate that the recent effective population size (Ne) of this species = 1.24 × 105, based on silent site diversity. We compare patterns of diversity in these genomes with patterns in multiple genome sequences of the house mouse (Mus musculus castaneus), which has a much larger Ne. This reveals an important role for variation in the strength of genetic drift in mammalian genome evolution. By a Pairwise Sequentially Markovian Coalescent (PSMC) analysis of demographic history, we infer that there has been a recent population size bottleneck in wild rats, which we date to approximately 20,000 years ago. Consistent with this, wild rat populations have experienced an increased flux of mildly deleterious mutations, which segregate at higher frequencies in protein-coding genes and conserved noncoding elements (CNEs). This leads to negative estimates of the rate of adaptive evolution (α) in proteins and CNEs, a result which we discuss in relation to the strongly positive estimates observed in wild house mice. As a consequence of the population bottleneck, wild rats also show a markedly slower decay of linkage disequilibrium with physical distance than wild house mice.
Pulmonary arterial development during childhood: branching pattern and structure

In lungs from 18 children aged between birth and 11 years the development of the branching pattern and structure of the pulmonary arteries, particularly the intralobular and intra-acinar, has been quantitatively analysed after injection with a radio-opaque medium. Up to 18 months of age as new alveolar ducts appear conventional arterial branches develop within the acinus: supernumerary arteries increase in number up to 8 years as new alveoli form. Both types increase in size with age. After birth there is an immediate drop in wall thickness of the vessels below 200 μm diameter while the larger vessels take up to 4 months to fall to adult thickness, suggesting two types of response—one dilatation, the other a growth rate change of the muscle cells. During childhood muscle cell formation in the intra-acinar arteries lags behind increase in artery size so that during childhood few muscular arteries are found within the acinus. The functional significance of these changes is discussed.
Rice–arsenate interactions in hydroponics: a three-gene model for tolerance

In this study, the genetic mapping of the tolerance of root growth to 13.3 μM arsenate [As(V)] using the Bala×Azucena population is improved, and candidate genes for further study are identified. A remarkable three-gene model of tolerance is advanced, which appears to involve epistatic interaction between three major genes, two on chromosome 6 and one on chromosome 10. Any combination of two of these genes inherited from the tolerant parent leads to the plant having tolerance. Lists of potential positional candidate genes are presented. These are then refined using whole genome transcriptomics data and bioinformatics. Physiological evidence is also provided that genes related to phosphate transport are unlikely to be behind the genetic loci conferring tolerance. These results offer testable hypotheses for genes related to As(V) tolerance that might offer strategies for mitigating arsenic (As) accumulation in consumed rice.
FLEXURAL REINFORCED CONCRETE MEMBERS WITH MINIMUM REINFORCEMENT UNDER LOW-VELOCITY IMPACT LOAD

Under various accidental situations, reinforced concrete members may be subjected to lowvelocity impact loading. To avoid the sudden failure due to high strain rate, an amount of reinforcement is required. This paper presents the finite element analysis of simple reinforced concrete beams under lowvelocity impact load. Falling weights of 250 and 500 kg were dropped at 1.2 m high on the beam midspan. Shear-to-bending capacity ratios varied from 0.9 to 11.3. Sixteen beams under different beam reinforcement ratios and with minimum static reinforcements were studied. The magnitude of the impact force, reactions, crack pattern, strains in beam reinforcements were examined. Shear crack, plastic strain in stirrups and shear plug damage were observed on the high flexural resistance specimens while the specimens with low flexural resistance completely failed in flexural failure. Finally, it could be concluded that the impact loading design requires more amount of reinforcement, especially transverse reinforcement to avoid the brittle shear failure. In addition, the longitudinal reinforcement should be increased to 2-4 times from the design in static load case to prevent sudden flexural failure of the structures.
Counterfeiting Detection in RFID-enabled Supply Chain

Counterfeiting is a generalized term which includes both the act of RFID tags, cloning and fraud. RFID tag counterfeiting attacks lead to financial losses, loss of trust and confidence in the adoption and acceptance of RFID technology. The challenge of implementing a cost-based counterfeit detection system in RFID supply chains is non-trivial because counterfeit tags exist across billions of RFID tags. In this paper, a cost-sensitive learning approach is presented. The motivation of this work is to effectively reduce the overall cost of counterfeiting attack for RFID tagged products. Experiments are conducted to present the efficiency, effectiveness, misclassification cost and test cost evaluations. Findings from this paper conclude that MetaCost learners provide the best result. However, when compared to AdaCost, MetaCost is more expensive in classifying counterfeit tags.
Unphosphorylated EIIANtr induces ClpAP‐mediated degradation of RpoS in Azotobacter vinelandii

The nitrogen‐related phosphotransferase system (PTSNtr) is composed of the EINtr, NPr and EIIANtr proteins that form a phosphorylation cascade from phosphoenolpyruvate. PTSNtr is a global regulatory system present in most Gram‐negative bacteria that controls some pivotal processes such as potassium and phosphate homeostasis, virulence, nitrogen fixation and ABC transport activation. In the soil bacterium Azotobacter vinelandii, unphosphorylated EIIANtr negatively regulates the expression of genes related to the synthesis of the bioplastic polyester poly‐β‐hydroxybutyrate (PHB) and cyst‐specific lipids alkylresorcinols (ARs). The mechanism by which EIIANtr controls gene expression in A. vinelandii is not known. Here, we show that, in presence of unphosphorylated EIIANtr, the stability of the stationary phase sigma factor RpoS, which is necessary for transcriptional activation of PHB and ARs synthesis related genes, is reduced, and that the inactivation of genes coding for ClpAP protease complex in strains that carry unphosphorylated EIIANtr, restored the levels and in vivo stability of RpoS, as well as the synthesis of PHB and ARs. Taken together, our results reveal a novel mechanism, by which EIIANtr globally controls gene expression in A. vinelandii, where the unphosphorylated EIIANtr induces the degradation of RpoS by the proteolytic complex ClpAP.