Miracle-dz/UniFAR-FTUs huggingface dataset:
SANA: simulated annealing far outperforms many other search algorithms for biological network alignment

Summary: Every alignment algorithm consists of two orthogonal components: an objective function M measuring the quality of an alignment, and a search algorithm that explores the space of alignments looking for ones scoring well according to M. We introduce a new search algorithm called SANA (Simulated Annealing Network Aligner) and apply it to protein‐protein interaction networks using S3 as the topological measure. Compared against 12 recent algorithms, SANA produces 5‐10 times as many correct node pairings as the others when the correct answer is known. We expose an anti‐correlation in many existing aligners between their ability to produce good topological vs. functional similarity scores, whereas SANA usually outscores other methods in both measures. If given the perfect objective function encoding the identity mapping, SANA quickly converges to the perfect solution while many other algorithms falter. We observe that when aligning networks with a known mapping and optimizing only S3, SANA creates alignments that are not perfect and yet whose S3 scores match that of the perfect alignment. We call this phenomenon saturation of the topological score. Saturation implies that a measure's correlation with alignment correctness falters before the perfect alignment is reached. This, combined with SANA's ability to produce the perfect alignment if given the perfect objective function, suggests that better objective functions may lead to dramatically better alignments. We conclude that future work should focus on finding better objective functions, and offer SANA as the search algorithm of choice. Availability and Implementation: Software available at http://sana.ics. uci.edu. Contact: whayes@uci.edu Supplementary information: Supplementary data are available at Bioinformatics online.
Draft Genome Sequence of Lactobacillus helveticus Strain Lh 12 Isolated from Natural Whey Starter

ABSTRACT Lactobacillus helveticus is a lactic acid bacterium widely used in cheese-making and for the production of bioactive peptides from milk proteins. Here, we describe the draft genome sequence and annotation of L. helveticus strain Lh 12 isolated from natural whey starter used in the production of Grana Padano cheese.
Muscle Oxygenation Responses to Low-intensity Steady Rate Concentric and Eccentric Cycling

Abstract Muscle deoxygenation responses provide information about the training impulse of an exercise session enabling adaptation to be predicted. Our aim was to investigate muscle oxygenation profiles during prolonged low-intensity eccentric and concentric cycling. Twelve healthy men performed two 45-min exercise sessions of concentric (CON) and eccentric (ECC) cycling, matched for the same heart rate at the start of each session. Mechanical power output during ECC was ~2.5 times that of CON (210±40 W vs. 82±16 W). Oxygen uptake, blood lactate, cardiac output and systolic arterial pressure responses did not differ between exercises. Heart rate was similar at 5 min of each exercise bout but progressively increased during ECC and was higher at 15, 30 and 45 min of ECC compared to CON (+10 bpm), with a trend for a lower stroke volume. Diastolic and mean blood pressures were higher during ECC. No significant differences were observed in muscle oxygenation profiles. Muscle oxygenation responses during prolonged low-intensity exercise were not affected by the type of muscle action at the same metabolic demand and cardiac output.
Exploring new quantitative CT image features to improve assessment of lung cancer prognosis

Due to the promotion of lung cancer screening, more Stage I non-small-cell lung cancers (NSCLC) are currently detected, which usually have favorable prognosis. However, a high percentage of the patients have cancer recurrence after surgery, which reduces overall survival rate. To achieve optimal efficacy of treating and managing Stage I NSCLC patients, it is important to develop more accurate and reliable biomarkers or tools to predict cancer prognosis. The purpose of this study is to investigate a new quantitative image analysis method to predict the risk of lung cancer recurrence of Stage I NSCLC patients after the lung cancer surgery using the conventional chest computed tomography (CT) images and compare the prediction result with a popular genetic biomarker namely, protein expression of the excision repair cross-complementing 1 (ERCC1) genes. In this study, we developed and tested a new computer-aided detection (CAD) scheme to segment lung tumors and initially compute 35 tumor-related morphologic and texture features from CT images. By applying a machine learning based feature selection method, we identified a set of 8 effective and non-redundant image features. Using these features we trained a naïve Bayesian network based classifier to predict the risk of cancer recurrence. When applying to a test dataset with 79 Stage I NSCLC cases, the computed areas under ROC curves were 0.77±0.06 and 0.63±0.07 when using the quantitative image based classifier and ERCC1, respectively. The study results demonstrated the feasibility of improving accuracy of predicting cancer prognosis or recurrence risk using a CAD-based quantitative image analysis method.
Midlife Work-Related Stress Increases Dementia Risk in Later Life: The CAIDE 30-Year Study

Objective To investigate the associations between midlife work-related stress and mild cognitive impairment (MCI), dementia, and Alzheimer's disease later in life, in a large representative population. Method Cardiovascular Risk Factors, Aging and Dementia (CAIDE) study participants were randomly selected from independent population-based surveys (mean age 50 years). A random sample of 2,000 individuals was invited for two reexaminations including cognitive tests (at mean age 71 and mean age 78), and 1,511 subjects participated in at least one reexamination (mean follow-up 28.5 years). Work-related stress was measured using two questions on work demands that were administered in midlife. Analyses adjusted for important confounders. Results Higher levels of midlife work-related stress were associated with higher risk of MCI (odds ratio [OR], 1.38; 95% confidence interval [CI], 1.08-1.76), dementia (OR, 1.53; CI, 1.13-2.07), and Alzheimer's disease (OR, 1.55; CI, 1.19-2.36) at the first follow-up among the CAIDE participants. Results remained significant after adjusting for several possible confounders. Work-related stress was not associated with MCI and dementia during the extended follow-up. Discussion Midlife work-related stress increases the risk for MCI, dementia, and Alzheimer's disease in later life. The association was not seen after the extended follow-up possibly reflecting selective survival/participation, heterogeneity in dementia among the oldest old, and a critical time window for the effects of midlife stress.
Fructose-containing caloric sweeteners as a cause of obesity and metabolic disorders

ABSTRACT Compared with other carbohydrates, fructose-containing caloric sweeteners (sucrose, high-fructose corn syrup, pure fructose and fructose-glucose mixtures) are characterized by: a sweet taste generally associated with a positive hedonic tone; specific intestinal fructose transporters, i.e. GLUT5; a two-step fructose metabolism, consisting of the conversion of fructose carbones into ubiquitous energy substrates in splanchnic organs where fructolytic enzymes are expressed, and secondary delivery of these substrates to extrasplanchnic tissues. Fructose is a dispensable nutrient, yet its energy can be stored very efficiently owing to a rapid induction of intestinal fructose transporters and of splanchnic fructolytic and lipogenic enzymes by dietary fructose-containing caloric sweeteners. In addition, compared with fat or other dietary carbohydrates, fructose may be favored as an energy store because it uses different intestinal absorption mechanisms and different inter-organ trafficking pathways. These specific features make fructose an advantageous energy substrate in wild animals, mainly when consumed before periods of scarcity or high energy turnover such as migrations. These properties of fructose storage are also advantageous to humans who are involved in strenuous sport activities. In subjects with low physical activity, however, these same features of fructose metabolism may have the harmful effect of favoring energy overconsumption. Furthermore, a continuous exposure to high fructose intake associated with a low energy turnover leads to a chronic overproduction of intrahepatic trioses-phosphate production, which is secondarily responsible for the development of hepatic insulin resistance, intrahepatic fat accumulation, and increased blood triglyceride concentrations. In the long term, these effects may contribute to the development of metabolic and cardiovascular diseases. Summary: Fructose is initially metabolized by fructolysis, gluconeogenesis or lipogenesis in the gut, liver and kidneys, and then made available as lactate, glucose and fatty acids in extrasplanchnic tissues. This two-step metabolism may have important functional consequences for health.
Activity Recognition for Persons With Stroke Using Mobile Phone Technology: Toward Improved Performance in a Home Setting

Background Smartphones contain sensors that measure movement-related data, making them promising tools for monitoring physical activity after a stroke. Activity recognition (AR) systems are typically trained on movement data from healthy individuals collected in a laboratory setting. However, movement patterns change after a stroke (eg, gait impairment), and activities may be performed differently at home than in a lab. Thus, it is important to validate AR for gait-impaired stroke patients in a home setting for accurate clinical predictions. Objective In this study, we sought to evaluate AR performance in a home setting for individuals who had suffered a stroke, by using different sets of training activities. Specifically, we compared AR performance for persons with stroke while varying the origin of training data, based on either population (healthy persons or persons with stoke) or environment (laboratory or home setting). Methods Thirty individuals with stroke and fifteen healthy subjects performed a series of mobility-related activities, either in a laboratory or at home, while wearing a smartphone. A custom-built app collected signals from the phone’s accelerometer, gyroscope, and barometer sensors, and subjects self-labeled the mobility activities. We trained a random forest AR model using either healthy or stroke activity data. Primary measures of AR performance were (1) the mean recall of activities and (2) the misclassification of stationary and ambulatory activities. Results A classifier trained on stroke activity data performed better than one trained on healthy activity data, improving average recall from 53% to 75%. The healthy-trained classifier performance declined with gait impairment severity, more often misclassifying ambulatory activities as stationary ones. The classifier trained on in-lab activities had a lower average recall for at-home activities (56%) than for in-lab activities collected on a different day (77%). Conclusions Stroke-based training data is needed for high quality AR among gait-impaired individuals with stroke. Additionally, AR systems for home and community monitoring would likely benefit from including at-home activities in the training data.
Hypoxia inducible factor-1α regulates autophagy via the p27-E2F1 signaling pathway

Autophagy is a highly conserved process by which the cell contents are delivered to lysosomes for degradation, or are used to provide macromolecules for energy generation under conditions of nutritional starvation. It has previously been demonstrated that cancer cells in hypoxic regions, with an oxygen concentration below the normal physiological level, express hypoxia inducible factor (HIF)-1α, in order to adapt and survive. HIF-1α is important in the regulation of oxygen homeostasis and the transcription of hundreds of genes in response to conditions of hypoxia, hence maintaining energy and redox homeostasis. To determine if HIF-1α modulates autophagy and the underlying molecular mechanisms regulating this process, the human esophageal cancer EC109 and IMR90 human diploid fibroblast cell lines were exposed to normoxic or hypoxic conditions and the expression levels of various proteins subsequently examined. Small interfering RNA was used to silence p27, in order to investigate its role in the process of HIF-1α regulated autophagy. Hypoxia induced autophagy in IMR90 cells and it was revealed that immature IMR90 cells demonstrated an increased rate of autophagy compared with mature cells. HIF-1α promoted EC109 cell autophagy via positively modulating p27, whereas silencing of p27 abolished the autophagy induced by hypoxia. The present study identified the primary components of the p27-E2F1 signaling pathway by which HIF-1α regulates autophagy. A previously unidentified mechanism is here presented, via which cancer cells may generate energy, or obtain macromolecules for survival.
Pulse transit time estimation from anacrotic photoplethysmography waveforms

Pulse transit time (PTT) is a useful marker that has been used by many researchers to indirectly estimate cardiovascular parameters. Photoplethysmogram (PPG) is one of the most common waveforms used for the estimation of PTT. In this paper, we propose a new method to estimate the PTT from the anacrotic phase of the PPG signal using autoregressive with exogenous (ARX) system identification approach. The results show that the proposed method produces lower model order, higher average model fitness and the resulting PTT values are in the same range of PTT values as estimated trough the traditional method.
Does Kin Recognition and Sib-Mating Avoidance Limit the Risk of Genetic Incompatibility in a Parasitic Wasp?

Background When some combinations of maternal and paternal alleles have a detrimental effect on offspring fitness, females should be able to choose mates on the basis of their genetic compatibility. In numerous Hymenoptera, the sex of an individual depends of the allelic combination at a specific locus (single-locus Complementary Sex Determination), and in most of these species individuals that are homozygous at this sexual locus develop into diploid males with zero fitness. Methods and Findings In this paper, we tested the hypothesis of genetic incompatibility avoidance by investigating sib-mating avoidance in the solitary wasp parasitoid, Venturia canescens. In the context of mate choice we show, for the first time in a non-social hymenopteran species, that females can avoid mating with their brothers through kin recognition. In “no-choice” tests, the probability a female will mate with an unrelated male is twice as high as the chance of her mating with her brothers. In contrast, in choice tests in small test arenas, no kin discrimination effect was observed. Further experiments with male extracts demonstrate that chemical cues emanating from related males influence the acceptance rate of unrelated males. Conclusions Our results are compatible with the genetic incompatibility hypothesis. They suggest that the female wasps recognize sibs on the basis of a chemical signature carried or emitted by males possibly using a “self-referent phenotype matching” mechanism.
Characterizing the influence of surface roughness and inclination on 3D vision sensor performance

This paper reports a methodology to evaluate the performance of 3D scanners, focusing on the influence of surface roughness and inclination on the number of acquired data points and measurement noise. Point clouds were captured of samples mounted on a robotic pan-tilt stage using an Ensenso active stereo 3D scanner. The samples have isotropic texture and range in surface roughness (Ra) from 0.09 to 0.46 μm. By extracting the point cloud quality indicators, point density and standard deviation, at a multitude of inclinations, maps of scanner performance are created. These maps highlight the performance envelopes of the sensor, the aim being to predict and compare scanner performance on real-world surfaces, rather than idealistic artifacts. The results highlight the need to characterize 3D vision sensors by their measurement limits as well as best-case performance, determined either by theoretical calculation or measurements in ideal circumstances.
The contribution of policy, law, management, research, and advocacy failings to the recent extinctions of three Australian vertebrate species

Extinctions typically have ecological drivers, such as habitat loss. However, extinction events are also influenced by policy and management settings that may be antithetical to biodiversity conservation, inadequate to prevent extinction, insufficiently resourced, or poorly implemented. Three endemic Australian vertebrate species—the Christmas Island pipistrelle (Pipistrellus murrayi), Bramble Cay melomys (Melomys rubicola), and Christmas Island forest skink (Emoia nativitatis)—became extinct from 2009 to 2014. All 3 extinctions were predictable and probably preventable. We sought to identify the policy, management, research, and other shortcomings that contributed to their extinctions or failed to prevent them. These included a lack within national environmental legislation and policy of explicit commitment to the prevention of avoidable extinctions, lack of explicit accountability, inadequate resources for conservation (particularly for species not considered charismatic or not of high taxonomic distinctiveness), inadequate biosecurity, a slow and inadequate process for listing species as threatened, recovery planning that failed to consider the need for emergency response, inability of researchers to identify major threatening factors, lack of public engagement and involvement in conservation decisions, and limited advocacy. From these 3 cases, we recommend: environmental policy explicitly seeks to prevent extinction of any species and provides a clear chain of accountability and an explicit requirement for public inquiry following any extinction; implementation of a timely and comprehensive process for listing species as threatened and for recovery planning; reservation alone not be assumed sufficient to maintain species; enhancement of biosecurity measures; allocation of sufficient resources to undertake actions necessary to prevent extinction; monitoring be considered a pivotal component of the conservation response; research provides timely identification of factors responsible for decline and of the risk of extinction; effective dissemination of research results; advocacy by an informed public for the recovery of threatened species; and public involvement in governance of the recovery process. These recommendations should be applicable broadly to reduce the likelihood and incidence of extinctions.
Quality of Life and Its Influencing Factors of Couples Referred to An Infertility Center in Shiraz, Iran

Background Infertility adversely affects quality of life (QoL). The present study aims to evaluate QoL and its associated factors among infertile couples. Materials and Methods In this cross-sectional study, the Fertility QoL (FertiQoL) instrument was used to measure QoL among 501 volunteer couples who attended the Infertility Clinic at the Mother and Child Hospital, Shiraz, Iran. We used an additional questionnaire to assess participants’ demographic and clinical characteristics. The relationship between the scores of QoL to the sociodemographic and treatment data was analysed. Results The subjects with lower income levels had lower relational, mind/body, emotional, and total core scores. Female participants without academic education had lower scores in the emotional subscale, while the male participants showed lower scores in emotional, mind/body, relational, social, and total QoL domains. Subjects who had undergone any type of treatment, including pharmacological treatment, intrauterine insemination (IUI), intra-cytoplasmic sperm injection (ICSI), and in vitro fertilization (IVF) showed significantly lower scores in the environmental domain. Participants with lower infertility duration obtained significantly greater QoL scores. Finally, tolerability, emotional, and environmental domains were significantly more desirable when the infertility problem was related to a male factor. Conclusion Infertile couples with shorter duration of infertility and male etiology have higher QoL. Lower academic education, lower income levels, or prior unsuccessful treatments are associated with lower QoL.
A New Reference Genome Assembly for the Microcrustacean Daphnia pulex

Comparing genomes of closely related genotypes from populations with distinct demographic histories can help reveal the impact of effective population size on genome evolution. For this purpose, we present a high quality genome assembly of Daphnia pulex (PA42), and compare this with the first sequenced genome of this species (TCO), which was derived from an isolate from a population with >90% reduction in nucleotide diversity. PA42 has numerous similarities to TCO at the gene level, with an average amino acid sequence identity of 98.8 and >60% of orthologous proteins identical. Nonetheless, there is a highly elevated number of genes in the TCO genome annotation, with ∼7000 excess genes appearing to be false positives. This view is supported by the high GC content, lack of introns, and short length of these suspicious gene annotations. Consistent with the view that reduced effective population size can facilitate the accumulation of slightly deleterious genomic features, we observe more proliferation of transposable elements (TEs) and a higher frequency of gained introns in the TCO genome.
Cognition-Based Semantic Annotation for Web Images

Due to the semantic gap between low-level visual features and high-level semantic content of images, the methods for image annotation based on low-level visual features, cannot well meet the requirement of knowledge discovery from web images. Therefore, the automatic acquisition for high-level semantic content of image has become a hot research topic. The traditional image annotation methods represent images only by a few keywords, which cannot completely describe and rationally organize the high-level semantics of images, so it will lose a great deal of semantic information. Based on the different levels and different aspects of web images, we propose a new method to express and organize the high-level semantic content of web images. The method expresses the different levels semantic content of one image as a three-level network, composed of background semantic level, complementary semantic level and fine-grained semantic level. The experimental results show that our method is effective and efficient on the image annotation.
Computational logic: its origins and applications

Computational logic is the use of computers to establish facts in a logical formalism. Originating in nineteenth century attempts to understand the nature of mathematical reasoning, the subject now comprises a wide variety of formalisms, techniques and technologies. One strand of work follows the ‘logic for computable functions (LCF) approach’ pioneered by Robin Milner, where proofs can be constructed interactively or with the help of users’ code (which does not compromise correctness). A refinement of LCF, called Isabelle, retains these advantages while providing flexibility in the choice of logical formalism and much stronger automation. The main application of these techniques has been to prove the correctness of hardware and software systems, but increasingly researchers have been applying them to mathematics itself.