Miracle-dz/UniFAR-FTUs huggingface dataset:
Asynchronous Parallel Generating Set Search for Linearly Constrained Optimization

We describe an asynchronous parallel derivative-free algorithm for linearly constrained optimization. Generating set search (GSS) is the basis of our method. At each iteration, a GSS algorithm computes a set of search directions and corresponding trial points and then evaluates the objective function value at each trial point. Asynchronous versions of the algorithm have been developed in the unconstrained and bound-constrained cases which allow the iterations to continue (and new trial points to be generated and evaluated) as soon as any other trial point completes. This enables better utilization of parallel resources and a reduction in overall run time, especially for problems where the objective function takes minutes or hours to compute. For linearly constrained GSS, the convergence theory requires that the set of search directions conforms to the nearby boundary. This creates an immediate obstacle for asynchronous methods where the definition of nearby is not well defined. In this paper, we develop an asynchronous linearly constrained GSS method that overcomes this difficulty and maintains the original convergence theory. We describe our implementation in detail, including how to avoid function evaluations by caching function values and using approximate lookups. We test our implementation on every CUTEr test problem with general linear constraints and up to 1000 variables. Without tuning to individual problems, our implementation was able to solve 95% of the test problems with 10 or fewer variables, 73% of the problems with 11-100 variables, and nearly half of the problems with 100-1000 variables. To the best of our knowledge, these are the best results that have ever been achieved with a derivative-free method for linearly constrained optimization. Our asynchronous parallel implementation is freely available as part of the APPSPACK software.
Diversity and metabolic impact of intestinal Lactobacillus species in healthy adults and the elderly

The present study aimed at assessing the counts and species distribution of intestinal lactobacilli and exploring if the data are associated with BMI and blood glucose level in healthy adults and elderly persons. The BMI (P < 0·01), the level of fasting blood glucose (P < 0·001) and the total counts of lactobacilli (P < 0·01 by bacteriology; P < 0·001 by real-time PCR) were higher in the elderly. The number of species in adults was lower (P < 0·05), who were more often colonised with Lactobacillus acidophilus (P = 0·031) and L. helveticus (P < 0·001). In contrast, L. plantarum (P = 0·035), L. paracasei (P < 0·001) and L. reuteri (P = 0·031) were more prevalent in the elderly. L. rhamnosus was detected in adults (P < 0·001), but not in any elderly person. BMI was associated with counts of lactobacilli, adjusted for age and sex (P = 0·008). The higher BMI in both groups of persons was associated with the presence of obligate homofermentative lactobacilli and L. sakei, both adjusted for age and sex. Plasma glucose values were positively correlated with BMI and negatively correlated with colonisation with L. paracasei (P = 0·0238) in adults and on the borderline with L. fermentum (P = 0·052) in the elderly. Thus, the species-specific PCR analysis of Lactobacillus sp. combined with viable plating data indicates substantial age-related structural differences in the intestinal lactobacilli communities. The higher counts of intestinal Lactobacillus sp. are associated with higher BMI and blood glucose content, while their specific fermentative groups and species of lactobacilli appear at different glucose levels both in adults and in the elderly.
Update on hepatic stellate cells: pathogenic role in liver fibrosis and novel isolation techniques

Hepatic stellate cells (HSCs), also called Ito cells or lipocytes, are vitamin A-storing cells located in the Dissé space between hepatocytes and sinusoidal endothelial cells. Upon liver injury, these cells transdifferentiate into extracellular matrix-producing, highly proliferative myofibroblasts that promote hepatic fibrogenesis. Other possible collagen-producing cells in liver fibrosis include portal fibroblasts, bone marrow-derived cells (mesenchymal stem cells, fibrocytes and hematopoietic cells) and parenchymal cells undergoing epithelial-to-mesenchymal transition. Important factors and signaling pathways for HSC activation, as well as different functions of HSC during homeostasis and fibrosis, such as collagen production, secretion of cytokines and chemokines, immune modulation and changes in contractile features, as well as vitamin A storage capacity, have been identified in vitro and in vivo. Novel isolation techniques, specifically HSC sorting by FACS via autofluorescence and antibodies, will provide us with further opportunities to advance our understanding of HSC biology in health and disease.
Analysis of Culex and Aedes mosquitoes in southwestern Nigeria revealed no West Nile virus activity

Introduction Amplification and transmission of West Nile virus (WNV) by mosquitoes are driven by presence and number of viraemic/susceptible avian hosts. Methods In order to predict risk of WNV infection to humans, we collected mosquitoes from horse stables in Lagos and Ibadan, southwestern Nigeria. The mosquitoes were sorted and tested in pools with real-time RT-PCR to detect WNV (or flavivirus) RNA using WNV-specific primers and probes, as well as, pan-flavivirus-specific primers in two-step real-time RT-PCR. Minimum infection rate (MIR) was used to estimate mosquito infection rate. Results Only two genera of mosquitoes were caught (Culex, 98.9% and Aedes, 1.0%) totalling 4,112 females. None of the 424 mosquito pools tested was positive for WNV RNA; consequently the MIR was zero. Sequencing and BLAST analysis of amplicons detected in pan-flavivirus primer-mediated RT-PCR gave a consensus sequence of 28S rRNA of Culex quinquefasciatus suggesting integration of flaviviral RNA into mosquito genome. Conclusion While the latter finding requires further investigation, we conclude there was little or no risk of human infection with WNV in the study areas during sampling. There was predominance of Culex mosquito, a competent WNV vector, around horse stables in the study areas. However, mosquito surveillance needs to continue for prompt detection of WNV activity in mosquitoes.
Contributions of structure and innervation pattern of the stick insect extensor tibiae muscle to the filter characteristics of the muscle-joint system

It is shown that the low-pass filter characteristics of the muscle­joint system of the femur­tibia joint of the stick insect Cuniculina impigra result from co-contraction of the extensor and flexor tibiae muscles. The most distal region of the extensor muscle, which contains a high percentage of slow muscle fibres, is involved in this co-contraction. This conclusion results from the following evidence. (1) Inertial and friction forces do not affect the characteristics of the low-pass filter of the muscle­joint system. (2) There is some co-contraction of the extensor and flexor muscles during sinusoidal stimulation of the femoral chordotonal organ at high stimulus frequencies. Both muscles generate tonic forces that increase with increasing stimulus frequency and also increase with time from the beginning of stimulation until a plateau is reached. (3) For the extensor muscle, this tonic force is produced by its most distal portion only. (4) Electrical stimulation of the common inhibitory motoneurone (CI1) reduces the tonic force generated in this most distal portion of the extensor muscle. Therefore, CI1 stimulation reduces the amplitude of tibial movement in response to sinusoidal stimulation of the femoral chordotonal organ at stimulus frequencies below 0.5 Hz (over this frequency range, the tibial movement amplitude is a function of the force amplitude produced by the whole extensor muscle and there is no co-contraction), but at chordotonal organ stimulus frequencies of 1 Hz and above, CI1 stimulation increases the tibial movement amplitude (in this case, movement amplitude is limited by the degree of co-contraction of the extensor and flexor muscles). With repeated chordotonal organ stimulation at higher stimulus frequencies, the tibial movement amplitude steadily decreases. This must be a consequence of increasing levels of co-contraction of the extensor and flexor muscles, since at low stimulus frequencies (no co-contraction) there is no reduction in movement amplitude during repeated stimulations. It is concluded that co-contraction of the extensor and flexor tibiae muscles prevents instability in the reflex loop in spite of the high gain necessary for the generation of catalepsy. Therefore, the mechanism described can be considered to be an adaptation to the ecological niche occupied by this animal. The contribution of the distal part of the extensor muscle to this system can be switched off by the CI1 during active movements.
Death‐associated protein kinase 1 variation and Parkinson’s disease

Background and purpose: Mutations of the LRRK2 gene are now recognized as major risk factors for Parkinson’s disease. The Lrrk2 protein is a member of the ROCO family, which also includes Lrrk1 and Dapk1. Functional genetic variants of the DAPK1 gene (rs4877365 and rs4878104) have been previously associated with Alzheimer’s disease.
Up-Regulation of Cyclooxygenase-2 Expression Is Involved in R(+)-Methanandamide-Induced Apoptotic Death of Human Neuroglioma Cells

Cannabinoids have been implicated in the reduction of glioma growth. The present study investigated a possible relationship between the recently shown induction of cyclooxygenase (COX)-2 expression by the endocannabinoid analog R(+)methanandamide [R(+)-MA] and its effect on the viability of H4 human neuroglioma cells. Incubation with R(+)-MA for up to 72 h decreased the cellular viability and enhanced accumulation of cytoplasmic DNA fragments in a time-dependent manner. Suppression of R(+)-MA-induced prostaglandin (PG) E2 synthesis with the selective COX-2 inhibitor celecoxib (0.01-1 μM) or inhibition of COX-2 expression by COX-2-silencing small-interfering RNA was accompanied by inhibition of R(+)-MA-mediated DNA fragmentation and cell death. In contrast, the selective COX-1 inhibitor SC-560 was inactive in this respect. Cells were also protected from apoptotic cell death by other COX-2 inhibitors (NS-398 {[N-[2-(cyclohexyloxy)-4-nitrophenyl]-methanesulfonamide]} and diclofenac) and by the ceramide synthase inhibitor fumonisin B1, which interferes with COX-2 expression by R(+)-MA. Moreover, the proapoptotic action of R(+)-MA was mimicked by the major COX-2 product PGE2. Apoptosis and cell death by R(+)-MA were not affected by antagonists of cannabinoid receptors (CB1, CB2) and vanilloid receptor 1. In further experiments, celecoxib was demonstrated to suppress apoptotic cell death elicited by anandamide, which is structurally similar to R(+)-MA. As a whole, this study defines COX-2 as a hitherto unknown target by which a cannabinoid induces apoptotic death of glioma cells. Furthermore, our data show that pharmacological concentrations of celecoxib may interfere with the proapoptotic action of R(+)-MA and anandamide, suggesting that cotreatment with COX-2 inhibitors could diminish glioma regression induced by these compounds.
Influence of Compactive Efforts on Lime-Slag Treated Tropical Black Clay

The results of a laboratory study on the influence of standard Proctor and West African Standard (WAS) compactive efforts on the compaction and strength characteristics of tropical black clay with a maximum of 8% lime and 10% slag (by dry weight of soil) is presented. Lime stabilized soil was admixed with slag in order to establish its soil improving potentials. Unconfined compressive strength and California bearing ratio tests on the soil-lime-slag mixtures yielded peak values at 8% lime and 7.5% slag concentrations in all the cases considered. The soil-lime-slag mixtures can be used as subbase and base courses of lightly trafficked roads when compacted at the energies of the standard Proctor and WAS, respectively.
Wideband Millimeter-Wave Propagation Measurements and Channel Models for Future Wireless Communication System Design

The relatively unused millimeter-wave (mmWave) spectrum offers excellent opportunities to increase mobile capacity due to the enormous amount of available raw bandwidth. This paper presents experimental measurements and empirically-based propagation channel models for the 28, 38, 60, and 73 GHz mmWave bands, using a wideband sliding correlator channel sounder with steerable directional horn antennas at both the transmitter and receiver from 2011 to 2013. More than 15,000 power delay profiles were measured across the mmWave bands to yield directional and omnidirectional path loss models, temporal and spatial channel models, and outage probabilities. Models presented here offer side-by-side comparisons of propagation characteristics over a wide range of mmWave bands, and the results and models are useful for the research and standardization process of future mmWave systems. Directional and omnidirectional path loss models with respect to a 1 m close-in free space reference distance over a wide range of mmWave frequencies and scenarios using directional antennas in real-world environments are provided herein, and are shown to simplify mmWave path loss models, while allowing researchers to globally compare and standardize path loss parameters for emerging mmWave wireless networks. A new channel impulse response modeling framework, shown to agree with extensive mmWave measurements over several bands, is presented for use in link-layer simulations, using the observed fact that spatial lobes contain multipath energy that arrives at many different propagation time intervals. The results presented here may assist researchers in analyzing and simulating the performance of next-generation mmWave wireless networks that will rely on adaptive antennas and multiple-input and multiple-output (MIMO) antenna systems.
Communications-Inspired Projection Design with Application to Compressive Sensing

We consider the recovery of an underlying signal $\mathbf{x}\in\mathbb{C}^m$ based on projection measurements of the form $\mathbf{y}=\mathbf{M}\mathbf{x}+\mathbf{w}$, where $\mathbf{y}\in\mathbb{C}^\ell$ and $\mathbf{w}$ is measurement noise; we are interested in the case $\ell\ll m$. It is assumed that the signal model $p(\mathbf{x})$ is known and that $\mathbf{w}\sim\mathcal{CN}(\mathbf{w};\boldsymbol{0},\bf \Sigma_w)$ for known $\bf \Sigma_w$. The objective is to design a projection matrix $\mathbf{M}\in\mathbb{C}^{\ell\times m}$ to maximize key information-theoretic quantities with operational significance, including the mutual information between the signal and the projections $\mathcal{I}(\mathbf{x};\mathbf{y})$ or the Renyi entropy of the projections $\mbox{h}_\alpha \left( \mathbf{y} \right)$ (Shannon entropy is a special case). By capitalizing on explicit characterizations of the gradients of the information measures with respect to the projection matrix, where we also partially extend the well-.
Primary mammary small-cell carcinoma: a molecular analysis of 2 cases.

Primary small-cell carcinoma of the breast is an exceedingly rare variant of breast carcinoma whose genetic profile has not been previously investigated. We report the molecular features of 2 cases of small-cell carcinoma of the breast: 1 with an adjacent intraductal carcinoma, and 1 with prior pleomorphic lobular carcinoma in situ. Laser capture microdissection followed by loss of heterozygosity (LOH) analysis revealed identical molecular alterations at multiple chromosomal regions, including BRCA-1, BRCA-2, p53, and retinoblastoma gene loci, in 1 case of small-cell carcinoma and its adjacent intraductal component. Additionally, LOH in 1 or both small-cell carcinomas was detected at 3p, 4q31.2-qter, 8p21-24, 11q13 (MEN-1 locus), 11q23.3, 11q24.1-25, 16q24.1 (H-cadherin locus), and 17q25. The results of our molecular analysis suggest that genetic changes in mammary small-cell carcinoma resembled those seen in both invasive ductal carcinomas and pulmonary small-cell carcinoma. Second, mammary small-cell carcinoma is clonally related to ductal carcinoma in situ and might represent an example of divergent differentiation occurring in a multipotential neoplastic stem cell.
Resolving the Vibrational and Electronic Contributions to Thermal Conductivity of Silicon Near the Solid-Liquid Transition: Molecular Dynamics Study

Although thermal transport in silicon is dominated by phonons in the solid state, electrons also participate as the system approaches, and exceeds, its melting point. Thus, the contribution from both phonons and electrons must be considered in any model for the thermal conductivity of silicon near the melting point. In this work, the phononic contribution to the bulk thermal conductivity of silicon is determined for the Stillinger-Weber potential in equilibrium and non-equilibrium molecular dynamics simulations for temperatures ranging from 1400 K to 2000 K. It is found that, although the contribution of electron-hole pair diffusion to high temperature conductivity of solid silicon is not included in classical molecular dynamics simulations, the Stillinger-Weber potential overestimates the vibrational contribution to thermal conductivity and, incidentally, reproduces quite well the total thermal conductivity of the solid phase up to the melting temperature. As for the liquid phase conductivity, the Stillinger-Weber potential agrees with theoretical treatment of the phononic thermal transport and predicts a minor phononic contribution of about 3% to the total liquid phase thermal conductivity. Thus, atomistic modeling of thermal transport in liquid phase silicon must include a description of the electronic contribution, e.g., through a combination of the molecular dynamics method with the continuum treatment of the electronic thermal conductivity within the two-temperature model.
Is there a Relationship between the Volume of Work Carried Out in Intensive Care and its Outcome?

Abstract This paper reports the results of a study of the association between volume of activity and patient outcome in 26 intensive care units in the United Kingdom. Hospital fatality rates showed a statistically significant (p =.016) negative association with volume. However, mean APACHE II scores, as a measure of the severity of case mix, were also negatively associated with volume (p =.021). Thus, one explanation of the lower death rates at higher volumes is that larger units admit less severely ill patients. For patients admitted immediately after surgery, the correlation between severity standardized mortality ratios and volume (while not significant, p <.1) suggests there may be a volume-output effect unexplained by severity.
Measurement of the intrinsic strength and intrinsic and total fracture resistances of stainless steel/E-glass composite joints

Parameters that characterize joint fracture are defined and procedures to measure them discussed. The interface strength σ o is measured by using a novel laser spallation experiment, which uses a laser-induced stress wave to separate the interface. The intrinsic (G ir) and total (G or) fracture resistances are measured using double cantilever beam experiments by carrying out these at cryogenic and ambient temperatures, respectively. These experiments are used to obtain hitherto unreported relationships between G or and G ir, and between σ o and G ir, for joints between stainless steel and E-glass composite sections. The durability of the joints under moisture exposure was also studied and was used as a means to alter σ o and G ir. Joint chemistries, including use of silane layers on the steel substrate, are disclosed which optimize the joint performance, with and without the preconditioning treatment of moisture exposure. In such optimized joints, the fracture is always cohesive within the composite adherend. The paper provides quantitative values for G ir, G or and σ o which are useful to a designer to set up the local failure condition in design simulations of ship structures in which such joints are considered as a part.
The Autophagic Process Occurs in Human Bone Metastasis and Implicates Molecular Mechanisms Differently Affected by Rab5a in the Early and Late Stages

Autophagy favours metastatic growth through fuelling energy and nutrients and resistance to anoikis, typical of disseminated-tumour cells. The autophagic process, mediated by a unique organelle, the autophagosome, which fuses with lysosomes, is divided into three steps. Several stages, especially early omegasome formation and isolation-membrane initiation, remain controversial; molecular mechanisms involve the small-GTPase Rab5a, which regulates vesicle traffic for autophagosome formation. We examined Rab5a involvement in the function of key members of ubiquitin-conjugation systems, Atg7 and LC3-lipidated, interacting with the scaffold-protein p62. Immunohistochemistry of Rab5a was performed in human specimens of bone metastasis and pair-matched breast carcinoma; the autophagic-molecular mechanisms affected by Rab5a were evaluated in human 1833 bone metastatic cells, derived from breast-carcinoma MDA-MB231 cells. To clarify the role of Rab5a, 1833 cells were transfected transiently with Rab5a-dominant negative, and/or stably with the short-hairpin RNA Atg7, were exposed to two inhibitors of autolysosome function, and LC3II and p62 expression was measured. We showed basal autophagy in bone-metastatic cells and the pivotal role of Rab5a together with Beclin 1 between the early stages, elongation of isolation membrane/closed autophagosome mediated by Atg7, and the late-degradative stages. This regulatory network might occur in bone-metastasis and in high-grade dysplastic lesions, preceding invasive-breast carcinoma and conferring phenotypic characteristics for dissemination.
Negative regulation of ABA signaling by WRKY33 is critical for Arabidopsis immunity towards Botrytis cinerea 2100

The Arabidopsis mutant wrky33 is highly susceptible to Botrytis cinerea. We identified >1680 Botrytis-induced WRKY33 binding sites associated with 1576 Arabidopsis genes. Transcriptional profiling defined 318 functional direct target genes at 14 hr post inoculation. Comparative analyses revealed that WRKY33 possesses dual functionality acting either as a repressor or as an activator in a promoter-context dependent manner. We confirmed known WRKY33 targets involved in hormone signaling and phytoalexin biosynthesis, but also uncovered a novel negative role of abscisic acid (ABA) in resistance towards B. cinerea 2100. The ABA biosynthesis genes NCED3 and NCED5 were identified as direct targets required for WRKY33-mediated resistance. Loss-of-WRKY33 function resulted in elevated ABA levels and genetic studies confirmed that WRKY33 acts upstream of NCED3/NCED5 to negatively regulate ABA biosynthesis. This study provides the first detailed view of the genome-wide contribution of a specific plant transcription factor in modulating the transcriptional network associated with plant immunity. DOI: http://dx.doi. org/10.7554/eLife.07295. 001