Miracle-dz/UniFAR-FTUs huggingface dataset:
Microbial eukaryote diversity in the marine oxygen minimum zone off northern Chile

Molecular surveys are revealing diverse eukaryotic assemblages in oxygen-limited ocean waters. These communities may play pivotal ecological roles through autotrophy, feeding, and a wide range of symbiotic associations with prokaryotes. We used 18S rRNA gene sequencing to provide the first snapshot of pelagic microeukaryotic community structure in two cellular size fractions (0.2–1.6 μm, >1.6 μm) from seven depths through the anoxic oxygen minimum zone (OMZ) off northern Chile. Sequencing of >154,000 amplicons revealed contrasting patterns of phylogenetic diversity across size fractions and depths. Protist and total eukaryote diversity in the >1.6 μm fraction peaked at the chlorophyll maximum in the upper photic zone before declining by ~50% in the OMZ. In contrast, diversity in the 0.2–1.6 μm fraction, though also elevated in the upper photic zone, increased four-fold from the lower oxycline to a maximum at the anoxic OMZ core. Dinoflagellates of the Dinophyceae and endosymbiotic Syndiniales clades dominated the protist assemblage at all depths (~40–70% of sequences). Other protist groups varied with depth, with the anoxic zone community of the larger size fraction enriched in euglenozoan flagellates and acantharean radiolarians (up to 18 and 40% of all sequences, respectively). The OMZ 0.2–1.6 μm fraction was dominated (11–99%) by Syndiniales, which exhibited depth-specific variation in composition and total richness despite uniform oxygen conditions. Metazoan sequences, though confined primarily to the 1.6 μm fraction above the OMZ, were also detected within the anoxic zone where groups such as copepods increased in abundance relative to the oxycline and upper OMZ. These data, compared to those from other low-oxygen sites, reveal variation in OMZ microeukaryote composition, helping to identify clades with potential adaptations to oxygen-depletion.
Kramers-Kronig relations and the properties of conductivity and permittivity in heterogeneous media

The macroscopic electric permittivity of a given medium may depend on frequency, but this frequency dependence cannot be arbitrary, its real and imaginary parts are related by the well-known Kramers-Kronig relations. Here, we show that an analogous paradigm applies to the macroscopic electric conductivity. If the causality principle is taken into account, there exists Kramers-Kronig relations for conductivity, which are mathematically equivalent to the Hilbert transform. These relations impose strong constraints that models of heterogeneous media should satisfy to have a physically plausible frequency dependence of the conductivity and permittivity. We illustrate these relations and constraints by a few examples of known physical media. These extended relations constitute important constraints to test the consistency of past and future experimental measurements of the electric properties of heterogeneous media.
Identification of Biomarkers Associated With Alzheimer’s Disease by Bioinformatics Analysis

Background: This study aimed to explore the biomarkers of Alzheimer’s disease (AD). Methods: The microarray data of GSE16759 were from the expression profile samples of 4 parietal lobe tissues from patients with AD and 4 ones from age-matched control participants. The differentially expressed micro RNAs (miRNAs) and genes (DEGs) underwent hierarchical clustering and function analysis followed by target genes prediction. Finally, DEGs were mapped to the target genes to construct miRNA-regulated networks. Results: A total of 427 DEGs were obtained and clustered into 5 functions. After DEGs were mapped to the predicted target genes, 313 regulatory pairs were established. The target genes SEC22 vesicle trafficking protein homolog B (SEC22B) and SEC63 homolog (SEC63) regulated by miRNA-206, RAB10, member RAS oncogene family (RAB10) regulated by miRNA-655, and fms-related tyrosine kinase 1 (FLT1) regulated by miRNA-30e-3p and miRNA-369-3p were involved in the biological processes of protein transport and regulation of cell motion. Conclusion: The target genes SEC22B, RAB10, and FLT1 may be potential biomarkers of AD.
Third-Party Data Providers Ruin Simple Mechanisms

Motivated by the growing prominence of third-party data providers in online marketplaces, this paper studies the impact of the presence of third-party data providers on mechanism design. When no data provider is present, it has been shown that simple mechanisms are "good enough'' -- they can achieve a constant fraction of the revenue of optimal mechanisms. The results in this paper demonstrate that this is no longer true in the presence of a third-party data provider who can provide the bidder with a signal that is correlated with the item type. Specifically, even with a single seller, a single bidder, and a single item of uncertain type for sale, the strategies of pricing each item-type separately (the analog of item pricing for multi-item auctions) and bundling all item-types under a single price (the analog of grand bundling) can both simultaneously be a logarithmic factor worse than the optimal revenue. Further, in the presence of a data provider, item-type partitioning mechanisms---a more general class of mechanisms which divide item-types into disjoint groups and offer prices for each group---still cannot achieve within a $łog łog$ factor of the optimal revenue. Thus, our results highlight that the presence of a data-provider forces the use of more complicated mechanisms in order to achieve a constant fraction of the optimal revenue.
Evaluating healthcare priority setting at the meso level: A thematic review of empirical literature

Background: Decentralization of health systems has made sub-national/regional healthcare systems the backbone of healthcare delivery. These regions are tasked with the difficult responsibility of determining healthcare priorities and resource allocation amidst scarce resources. We aimed to review empirical literature that evaluated priority setting practice at the meso (sub-national) level of health systems. Methods: We systematically searched PubMed, ScienceDirect and Google scholar databases and supplemented these with manual searching for relevant studies, based on the reference list of selected papers. We only included empirical studies that described and evaluated, or those that only evaluated priority setting practice at the meso-level. A total of 16 papers were identified from LMICs and HICs. We analyzed data from the selected papers by thematic review. Results: Few studies used systematic priority setting processes, and all but one were from HICs. Both formal and informal criteria are used in priority-setting, however, informal criteria appear to be more perverse in LMICs compared to HICs. The priority setting process at the meso-level is a top-down approach with minimal involvement of the community. Accountability for reasonableness was the most common evaluative framework as it was used in 12 of the 16 studies. Efficiency, reallocation of resources and options for service delivery redesign were the most common outcome measures used to evaluate priority setting. Limitations: Our study was limited by the fact that there are very few empirical studies that have evaluated priority setting at the meso-level and there is likelihood that we did not capture all the studies. Conclusions: Improving priority setting practices at the meso level is crucial to strengthening health systems. This can be achieved through incorporating and adapting systematic priority setting processes and frameworks to the context where used, and making considerations of both process and outcome measures during priority setting and resource allocation.
Fabrication and Biocompatibility of Carbon Nanotube-Based 3D Networks as Scaffolds for Cell Seeding and Growth

Thin film networks of multiwalled carbon nanotubes (MWCNTs) were prepared by exerting chemically induced capillary forces upon the nanotubes. During this process MWCNTs undergo a transformation from being a vertically aligned structure to an interlocking resistive network of interconnected nanotubes, whose main feature is a regular three-dimensional (3D) sieve architecture. Due to their structural characteristics at the nanoscale level, 3D-MWCNT-based networks are in principle ideal candidates for scaffolds/matrices in tissue engineering. Their potential application in this field was confirmed by extensive growth, spreading, and adhesion of the common mouse fibroblast cell line L929.
An Interactive Simulator for Imposing Virtual Musculoskeletal Dynamics

Objective: disease processes are often marked by both neural and muscular changes that alter movement control and execution, but these adaptations are difficult to tease apart because they occur simultaneously. This is addressed by swapping an individual's limb dynamics with a neurally controlled facsimile using an interactive musculoskeletal simulator (IMS) that allows controlled modifications of musculoskeletal dynamics. This paper details the design and operation of the IMS, quantifies and describes human adaptation to the IMS, and determines whether the IMS allows users to move naturally, a prerequisite for manipulation experiments. Methods: healthy volunteers (n = 4) practiced a swift goal-directed task (back-and-forth elbow flexion/extension) for 90 trials with the IMS off (normal dynamics) and 240 trials with the IMS on, i.e., the actions of a user's personalized electromyography-driven musculoskeletal model are robotically imposed back onto the user. Results: after practicing with the IMS on, subjects could complete the task with end-point errors of 1.56°, close to the speed-matched IMS-off error of 0.57°. Muscle activity, joint torque, and arm kinematics for IMS-on and -off conditions were well matched for three subjects (root-mean-squared error [RMSE] = 0.16 N·m), but the error was higher for one subject with a small stature (RMSE = 0.25 N·m). Conclusion: a well-matched musculoskeletal model allowed IMS users to perform a goal-directed task nearly as well as when the IMS was not active. Significance: this advancement permits real-time manipulations of musculoskeletal dynamics, which could increase our understanding of muscular and neural co-adaptations to injury, disease, disuse, and aging.
Environmental Drivers and Predicted Risk of Bacillary Dysentery in Southwest China

Bacillary dysentery has long been a considerable health problem in southwest China, however, the quantitative relationship between anthropogenic and physical environmental factors and the disease is not fully understand. It is also not clear where exactly the bacillary dysentery risk is potentially high. Based on the result of hotspot analysis, we generated training samples to build a spatial distribution model. Univariate analyses, autocorrelation and multi-collinearity examinations and stepwise selection were then applied to screen the potential causative factors. Multiple logistic regressions were finally applied to quantify the effects of key factors. A bootstrapping strategy was adopted while fitting models. The model was evaluated by area under the receiver operating characteristic curve (AUC), Kappa and independent validation samples. Hotspot counties were mainly mountainous lands in southwest China. Higher risk of bacillary dysentery was found associated with underdeveloped socio-economy, proximity to farmland or water bodies, higher environmental temperature, medium relative humidity and the distribution of the Tibeto-Burman ethnicity. A predictive risk map with high accuracy (88.19%) was generated. The high-risk areas are mainly located in the mountainous lands where the Tibeto-Burman people live, especially in the basins, river valleys or other flat places in the mountains with relatively lower elevation and a warmer climate. In the high-risk areas predicted by this study, improving the economic development, investment in health care and the construction of infrastructures for safe water supply, waste treatment and sewage disposal, and improving health related education could reduce the disease risk.
Reports on Progress in Physics REPORT ON PROGRESS Single-molecule techniques in biophysics : a review of the progress in methods and applications

Single-molecule biophysics has transformed our understanding of biology, but also of the physics of life. More exotic than simple soft matter, biomatter lives far from thermal equilibrium, covering multiple lengths from the nanoscale of single molecules to up to several orders of magnitude higher in cells, tissues and organisms. Biomolecules are often characterized by underlying instability: multiple metastable free energy states exist, separated by levels of just a few multiples of the thermal energy scale kBT, where kB is the Boltzmann constant and T absolute temperature, implying complex inter-conversion kinetics in the relatively hot, wet environment of active biological matter. A key benefit of single-molecule biophysics techniques is their ability to probe heterogeneity of free energy states across a molecular population, too challenging in general for conventional ensemble average approaches. Parallel developments in experimental and computational techniques have catalysed the birth of multiplexed, correlative techniques to tackle previously intractable biological questions. Experimentally, progress has been driven by improvements in sensitivity and speed of detectors, and the stability and efficiency of light sources, probes and microfluidics. We discuss the motivation and requirements for these recent experiments, including the underpinning mathematics. These methods are broadly divided into tools which detect molecules and those which manipulate them. For the former we discuss the progress of super-resolution microscopy, transformative for addressing many longstanding questions in the life sciences, and for the latter we include progress in ‘force spectroscopy’ techniques that mechanically perturb molecules. We also consider in silico progress of single-molecule computational physics, and how simulation and experimentation may be drawn together to give a more complete understanding. Increasingly, combinatorial techniques are now used, including correlative atomic force microscopy and fluorescence imaging, to probe questions closer to native physiological behaviour. We identify the trade-offs, limitations and applications of these techniques, and discuss exciting new directions.
Review article: liver transplantation for hepatocellular carcinoma – a critical appraisal of the current worldwide listing criteria

Liver transplantation (LT) plays an important role in the management of patients with hepatocellular carcinoma (HCC). Although early results following LT for HCC were poor, since the introduction of the Milan criteria in 1996 morphological criteria have since been well established. Thereafter, various expansions of the Milan criteria were introduced worldwide. Listing criteria for LT for HCC in the United Kingdom (UK) initially conformed to the Milan criteria but were re‐defined in 2009 by expansion of the Milan criteria.
The ketogenic and related diets in adolescents and adults—A review

The ketogenic diet (KD) has been used to treat children with epilepsy who are resistant to antiepileptic drugs (AEDs) since the 1920s, and has undergone a resurgence in popularity over the last 15 years Its use in adolescents and adults has been more restrained. During the past few decades, more liberal regimens have emerged that may seem more attractive to older people while still proving effective, often independent of ketone levels. The KD and its variants may lead to similar reductions in seizure frequency in adolescents and adults as seen in children, although studies are limited and of poor quality. A total of only 122 adults and 82 adolescents have been included in open‐label studies on the KD, and only 56 adults and 10 adolescents on the Modified Atkins Diet. Side effects appear similar to those encountered in children. Noncompliance may be higher in adolescents and adults than in children, but the main reason for discontinuation is lack of efficacy. A better understanding of the mechanisms underlying the effects of the KD might allow the same treatment effects to be achieved using novel, better‐tolerated, nondietary approaches.
Characterization of a Blood Spot Creatine Kinase Skeletal Muscle Isoform Immunoassay for High-Throughput Newborn Screening of Duchenne Muscular Dystrophy.

BACKGROUND Duchenne muscular dystrophy (DMD) is a progressive, lethal X-linked neuromuscular disorder with an average worldwide incidence of 1:5000. Blood spot creatine kinase (CK) enzyme assays previously used in newborn screening programs for DMD are nonspecific because measured CK enzyme activity is attributable to 3 isoenzyme forms of CK (CK-MM, CK-MB, and CK-BB) and it is the CK-MM isoform that is found predominantly in skeletal muscle. CK-MM is increased in boys with DMD owing to muscle damage. We describe a sensitive and specific automated immunoassay for CK-MM to screen for DMD in blood spots. METHODS The prototype assay was developed on the PerkinElmer GSP® analyzer to enable high-throughput screening. CK-MM was assayed using a solid phase, 2-site immunofluorometric system. Purified human CK-MM was used to create calibrators and controls. RESULTS The limit of blank (LOB), detection (LOD), and quantification (LOQ) values were <1, 3, and 8 ng/mL, respectively. The analytical measurement range was 4-8840 ng/mL. Interassay (n = 40) imprecision was <7% across the analytical range. Cross-reactivity was <5% for CK-MB and 0% for CK-BB. The mean recovery of CK-MM was 101% (range 87%-111%). Blood spots from newborn infants (n = 277) had a mean CK-MM concentration of 155 ng/mL and a 99th centile of 563 ng/mL. The mean blood spot CK-MM concentration from 10 cases of DMD was 5458 ng/mL (range 1217-9917 ng/mL). CONCLUSIONS CK-MM can be reliably quantified in blood spots. The development of this CK-MM assay on a commercial immunoassay analyzer would enable standardized and high-throughput newborn blood spot screening of DMD.
Analytics of deep neural network in change detection

Recently, deep neural networks (DNNs) have demonstrated excellent performance for change detection. The DNN-based background subtraction automatically discovers background features from datasets and outperforms traditional background modeling based on handcraft features and/or subtraction strategies. Most researchers mainly discuss the accuracy of foreground detection and do not analyze how and why the DNN works well for change detection tasks. It is necessary to understand what the DNN learns as background features in order to discuss the potential of the DNN in background subtraction. In this paper, we focus on the filters in the first convolution layer and the activations of neurons in the last fully connected layer to understand the behavior of the DNN. From the experiment, we found that 1) the first layer performs the role of background subtraction using several filters, and 2) the last layer categorizes some background changes into a group without supervised signals. These findings suggest the possibility of a new background modeling strategy based on data-driven extracted features.
Elevated Serum Carboxymethyl-Lysine, an Advanced Glycation End Product, Predicts Severe Walking Disability in Older Women: The Women's Health and Aging Study I

Advanced glycation end products (AGEs) have been implicated in the pathogenesis of sarcopenia. Our aim was to characterize the relationship between serum carboxymethyl-lysine (CML), a major circulating AGE, and incident severe walking disability (inability to walk or walking speed <0.4 m/sec) over 30 months of followup in 394 moderately to severely disabled women, ≥65 years, living in the community in Baltimore, Maryland (the Women's Health and Aging Study I). During followup, 154 (26.4%) women developed severe walking disability, and 23 women died. Women in the highest quartile of serum CML had increased risk of developing of severe walking disability in a multivariate Cox proportional hazards model, adjusting for age and other potential confounders. Women with elevated serum CML are at an increased risk of developing severe walking disability. AGEs are a potentially modifiable risk factor. Further work is needed to establish a causal relationship between AGEs and walking disability.
Mechanical Properties of Plied Cotton Fabric-Coated Unsaturated Polyester Composites: Effects of Alkali Treatments

This paper presents an experimental investigation on the mechanical properties of cotton fabric/polyester composites. Plied yarns (4-plies) of known count were woven and knitted into fabrics of different architectures. The cotton fabrics were subjected to chemical modifications using sodium hydroxide and its influence on some mechanical properties were analyzed. The fabrics were coated with unsaturated polyester resin as matrix. The tensile and flexural properties, impact strength and hardness of the textile composites were studied. Result indicated that alkali treatment improved the tensile strength and breaking elongation of the fabrics. The mechanical properties were found to depend on the fabric architecture; plying and fabrication conferred significant reinforcement on the composites for the different mechanical properties tested, which is an indication that woven and knitted cotton fabrics can function as reinforcement in textile composites. Increase in number of fabric layers brought about a corresponding increase in mechanical properties. Morphological studies showed that composites with treated fabrics exhibited better interfacial bonding between the matrix and reinforcement compared to other combinations as evidenced by less cracking of the matrix before fracture.
Optimizing the first-line fertility treatment

Abstract The objective of this study was to identify sperm score thresholds to achieve satisfactory intrauterine insemination (IUI) success rates according to the response to stimulation with clomiphene citrate (CC). To minimize the confounding effect of female age, we included only CC/IUI cycles of women ≤35 years old. A total of 1,194 CC/IUI cycles were included. Semen volume, concentration, and motility influenced the clinical pregnancy rate (CPR). Normal morphology (≥4%) was associated with a comparable CPR with 3%, 2%, and 1% normal forms (15.6%, 16.1%, 18.1%, and 13.1%, respectively). A combination of the total number of motile spermatozoa in the ejaculate before semen preparation (TM) at a threshold ≥20 × 106 was associated with a CPR of 17.8% compared to 4.6% for a threshold <20 × 106 (p < .001). Interestingly, the TM threshold to achieve satisfactory outcomes was lower (10 × 106) in patients who had an optimal response to CC (≥2 dominant follicles with an endometrial thickness ≥7 mm) compared to 40 × 106 for those who had a suboptimal response (one dominant follicle with an endometrial thickness <7 mm). In conclusion, the response to superovulation with CC determines each patient’s TM threshold required for satisfactory outcomes. Couples whose TM is below the threshold may benefit from a superovulation with gonadotropins or in vitro fertilization.
Characteristics Analysis of SPMSM Using 2-D Finite-Element Analysis Considering Axial Leakage Flux

In this paper, the characteristics analysis of the surface-mounted permanent-magnet synchronous motor is carried out using the method of reflecting the axial leakage magnetic flux into the 2-D finite-element analysis (2-D FEA), and the result is discussed. For the method of projecting the axial leakage flux on the 2-D plane, the permeance coefficient was introduced. By using the proposed method, the parameters such as d- and q-axes inductance and linkage flux for d- and q-axes equivalent circuit analysis were calculated, and the characteristics analysis was performed. In order to verify the effectiveness of the proposed 2-D FEA, a speed versus torque experiment was performed and compared with the analysis results.