Miracle-dz/UniFAR-FTUs huggingface dataset:
Sperm Motility Annotated Genes: Are They Associated with Impaired Fecundity?

Sperm motility is a prerequisite for achieving pregnancy, and alterations in sperm motility, along with sperm count and morphology, are commonly observed in subfertile men. The aim of the study was to determine whether the expression level of genes annotated with the Gene Ontology (GO) term ‘sperm motility’ differed in sperm collected from healthy men and men diagnosed with oligoasthenozoospermia. Reverse transcription quantitative real-time PCR (RT-qPCR), quantitative mass spectrometry (LC-MS/MS), and enrichment analyses were used to validate a set of 132 genes in 198 men present at an infertility clinic. Out of the 132 studied sperm-motility-associated genes, 114 showed differentially expressed levels in oligoasthenozoospermic men compared to those of normozoospermic controls using an RT-qPCR analysis. Of these, 94 genes showed a significantly lower expression level, and 20 genes showed a significantly higher expression level. An MS analysis of sperm from an independent cohort of healthy and subfertile men identified 692 differentially expressed proteins, of which 512 were significantly lower and 180 were significantly higher in oligoasthenozoospermic men compared to those of the normozoospermic controls. Of the 58 gene products quantified with both techniques, 48 (82.75%) showed concordant regulation. Besides the sperm-motility-associated proteins, the unbiased proteomics approach uncovered several novel proteins whose expression levels were specifically altered in abnormal sperm samples. Among these deregulated proteins, there was a clear overrepresentation of annotation terms related to sperm integrity, the cytoskeleton, and energy-related metabolism, as well as human phenotypes related to spermatogenesis and sperm-related abnormalities. These findings suggest that many of these proteins may serve as diagnostic markers of male infertility. Our study reveals an extended number of sperm-motility-associated genes with altered expression levels in the sperm of men with oligoasthenozoospermia. These genes and/or proteins can be used in the future for better assessments of male factor infertility.
Clinical guideline on magnetically controlled capsule gastroscopy (2021 edition)

With the development and generalization of endoscopic technology and screening, clinical application of magnetically controlled capsule gastroscopy (MCCG) has been increasing. In recent years, various types of MCCG are used globally. Therefore, establishing relevant guidelines on MCCG is of great significance. The current guidelines containing 23 statements were established based on clinical evidence and expert opinions, mainly focus on aspects including definition and diagnostic accuracy, application population, technical optimization, inspection process, and quality control of MCCG. The level of evidence and strength of recommendations were evaluated. The guidelines are expected to guide the standardized application and scientific innovation of MCCG for the reference of clinicians.
Severe wildfires promoted by climate change negatively impact forest amphibian metacommunities

Changes to the extent and severity of wildfires driven by anthropogenic climate change are predicted to have compounding negative consequences for ecological communities. While there is evidence that severe weather events like drought impact amphibian communities, the effects of wildfire on such communities are not well understood. The impact of wildfire on amphibian communities and species is likely to vary, owing to the diversity of their life‐history traits. However, no previous research has identified commonalities among the amphibians at most risk from wildfire, limiting conservation initiatives in the aftermath of severe wildfire. We aimed to investigate the impacts of the unprecedented 2019–2020 black summer bushfires on Australian forest amphibian communities.
Prevalence of familial hypercholesterolemia and its association with coronary artery disease: A Chinese cohort study

Abstract Background Familial hypercholesterolemia (FH) is underrecognized, and its association with coronary artery disease (CAD) remains limited, especially in China. We aimed to investigate the prevalence of FH and its relationship with CAD in a large Chinese cohort. Methods FH was defined using the Make Early Diagnosis to Prevent Early Death (MEDPED) criteria. The crude and age‐sex standardized prevalence of FH were calculated based on surveys of the Prediction for Atherosclerotic Cardiovascular Disease Risk in China (China‐PAR) project during 2007−2008. The associations of FH with incident CAD and its major subtypes were estimated with the cohort‐stratified multivariate Cox proportional hazard models based on the data from the baseline to the last follow‐up (2018−2020). Results Among 98,885 included participants, 190 participants were defined as FH. Crude and age−sex standardized prevalence and 95% confidence interval (CI) of FH were 0.19% (0.17%–0.22%) and 0.13% (0.10%–0.16%), respectively. The prevalence varied across age groups and peaked in the group of 60–<70 years (0.28%), and the peak prevalence (0.18%) in males was earlier, yet lower than the peak crude prevalence in females (0.41%). During a mean follow‐up of 10.7 years, 2493 cases of incident CAD were identified. After multivariate adjustment, FH patients had a 2.03‐fold greater risk of developing CAD compared to non‐FH participants. Conclusions The prevalence of FH was estimated to be 0.19% in the participants, and it was associated with an elevated risk of incident CAD. Our study suggests that early screening of FH has certain public health significance for the prevention of CAD.
Recent developments of bulk thermoelectric materials

A brief overview is given of several types of thermoelectric materials,including the standard Bi2Te3,PbTe and SiGe,common structures such as the skutterudites,clathrates,half-Heusler intermetallic compounds,metal oxides and Zn4Sb3-type compounds,as well as types with various new crystal structures.The crystal structure and optimization of the thermoelectric properties of these materials are discussed.
Investigation of Program Efficiency Overshoot in 3D Vertical Channel NAND Flash with Randomly Distributed Traps

The incremental step pulse programming slope (ISPP) with random variation was investigated by measuring numerous three−dimensional (3D) NAND flash memory cells with a vertical nanowire channel. We stored multiple bits in a cell with the ISPP scheme and read each cell pulse by pulse. The excessive tunneling from the channel to the storage layer determines the program efficiency overshoot. Then, a broadening of the threshold voltage distribution was observed due to the abnormal program cells. To analyze the randomly varying abnormal program behavior itself, we distinguished between the read variation and over−programming in measurements. Using a 3D Monte−Carlo simulation, which is a probabilistic approach to solve randomness, we clarified the physical origins of over−programming that strongly influence the abnormal program cells in program step voltage, and randomly distributed the trap site in the nitride of a nanoscale 3D NAND string. These causes have concurrent effects, but we divided and analyzed them quantitatively. Our results reveal the origins of the variation and the overshoot in the ISPP, widening the threshold voltage distribution with traps randomly located at the nanoscale. The findings can enhance understanding of random over−programming and help mitigate the most problematic programming obstacles for multiple−bit techniques.
Interactions of the main pathogenic fungi of papaya (Carica papaya, L.) as a function of temperature

Abstract The temperature effect on the interaction between fungal isolates of papaya was studied. Rhizopus stolonifer, Colletotrichum cobbittiense, Fusarium pernambucarum, and Alternaria arborescens were grown in papaya agar in pairs, one against the other, at 13, 25, and 35 °C. The growth rate for each fungus was compared when grown alone or paired. Four types of interaction were observed: mutual intermingling, mutual antagonism on contact, dominance on contact, and dominance at a distance. At 13 and 35 °C, F. pernambucarum was more competitive whereas at 25 °C R. stolonifer does. In vivo validation showed R. stolonifer was the dominant fungus at 25 °C but coexists with C. cobbittiense forming a second infection. Then, a hierarchy may be established through a growth mechanism to infer which fungi may develop first and damage fruit to prevent postharvest losses. These findings could improve the management of papaya fruit in the postharvest stage. HIGHLIGHTS Several species of fungi are responsible for postharvest diseases in papaya. Diseases development depends on environmental and fruit physiological conditions. One species may dominate or inhibit other’s or can coexist as well. Interactions between pathogenic fungi may be considered to infer fungi development. These results may help us to improve the postharvest treatment of papaya.
Genome-wide diversity and demographic dynamics of Cameroon goats and their divergence from east African, north African, and Asian conspecifics

Indigenous goats make significant contributions to Cameroon’s national and local economy, but little effort has been devoted to identifying the populations. Here, we assessed the genetic diversity and demographic dynamics of Cameroon goat populations using mitochondrial DNA (two populations) and autosomal markers (four populations) generated with the Caprine 50K SNP chip. To infer genetic relationships at continental and global level, genotype data on six goat populations from Ethiopia and one population each from Egypt, Morocco, Iran, and China were included in the analysis. The mtDNA analysis revealed 83 haplotypes, all belonging to haplogroup A, in Cameroon goats. Four haplotypes were shared between goats found in Cameroon, Mozambique, Namibia, Zimbabwe, Kenya, and Ethiopia. Analysis of autosomal SNPs in Cameroon goats revealed the lowest HO (0.335±0.13) and HE (0.352±0.15) in the North-west Highland and Central Highland populations, respectively. Overall, the highest HO (0.401±0.12) and HE (0.422±0.12) were found for Barki and Iranian goats, respectively. Barki goats had the highest average MAF, while Central Highland Cameroon goats had the lowest. Overall, Cameroon goats demonstrated high FIS. AMOVA revealed that 13.29% of the variation was explained by genetic differences between the six population groups. Low average FST (0.01) suggests intermixing among Cameroon goats. All measures indicated that Cameroon goats are closer to Moroccan goats than to other goat populations. PCA and STRUCTURE analyses poorly differentiated the Cameroon goats, as did genetic distance, Neighbor-Net network, and neighbor-joining tree analyses. The haplotype analysis of mtDNA showed the initial dispersion of goats to Cameroon and central Africa from north-east Africa following the Nile Delta. Whereas, the approximate Bayesian computation indicated Cameroon goats were separated from Moroccan goats after 506 generations in later times (~1518 YA), as supported by the phylogenetic net-work and admixture outputs. Overall, indigenous goats in Cameroon show weak phylogenetic structure, suggesting either extensive intermixing.
Design and development of cost-effective fiber Bragg grating temperature sensor package

A cost-effective fiber Bragg grating (FBG) temperature sensor package was designed and developed with two distinct sensing probes and demodulation schemes. U-shaped and capillary shape probes were designed and tested using an optical spectrum analyzer and two different indiginously developed intensity demodulation schemes. The temperature sensitivities were measured as 12.94 ± 0.15 pm °C−1, 11.57 ± 0.12 pm °C−1, and 12.03 ± 0.14 pm °C−1 for a bare FBG and for FBGs encapsulated in the U-shaped and capillary probes, respectively, with negligible hysteresis and a repeatability of 1 °C–3 °C. The performance of the probes was demonstrated by twin-FBG intensity demodulation schemes, the range of which was increased up to 181.50 °C with a resolution of 0.120 °C by the development of a CFBG-FBG intensity demodulation scheme.
Algorithms and hardness results in computational homology

In this thesis, we address various issues concerning characterizing topological features in computation. First, we define metrics on homology classes. This definition uses the discrete metric and the induced geodesic distance. A polynomial algorithm is provided to compute these measure. Besides, this work leads to the definition and algorithm of a canonical basis of the homology group, namely, the optimal homology basis. A straightforward algorithm and an improved algorithm are given. Second, we discuss the problem of homology localization, namely, localizing a homology class with a cycle which is concise in geometry. This problem is posed as an optimization problem. Different objective function is discussed. For the volume function, we show that the problem is NP-hard to approximate within constant factor. Other objective functions are also discussed, namely, the diameter and the radius. Third, we study the problem of enriching persistent homology. The objective is to reveal structural relationship between persistent homology classes by computing canonical representative cycles. Various definitions are provided basing on an extension of persistent homology. However, it has been proven that these definitions are not stable with regard to the change of filter function. Fourth, we apply computation topology method in ribosome drug docking problem. More specifically, we compute the pockets/cavities relating to the drug docking sites. Interesting insights about ribosome are revealed by our work. However, the results are not specific enough for studying drug docking sites.
Using Crowdsourced Data to Reduce Traffic Congestion by Improving Detection of and Response to Disabled or Abandoned Vehicles on Florida Limited-Access Facilities

Disabled or abandoned vehicles (DAVs) cause a significant proportion of non-recurring traffic congestion. Waze data has the potential to help traffic management center (TMC) operators detect and respond to DAVs more quickly, reducing congestion. Previous studies have examined Waze data on a small scale, but not at a statewide level. This paper analyzes over 2 years of DAV Waze data on Florida Department of Transportation (FDOT) limited-access roadways (with more than 10 million alerts) and compares them with reported DAV events (crashes and non-crash TMC reports). Over 46% of the DAV events had an associated Waze alert before the DAV event occurred, indicating significant potential for earlier detection. These Waze alerts typically happened about 16 min before the DAV event and were most common during daytime hours and in urban areas. Two roadway segments, I-4 in FDOT District 5 and State Road 91 (SR-91) in FDOT District 4, were examined in more detail. A methodology was developed to estimate the delay reduction and congestion savings achieved by the earlier detection provided by the Waze alerts for lane-blocking and shoulder-blocking disabled vehicle events. The estimated congestion savings for the second half of 2019 were $4.3 million (I-4) and $2.5 million (SR-91), with benefit-cost ratios of 61 and 27, respectively. An additional $4.3 million could potentially have been saved as a result of Waze alerts allowing responders to reach DAVs before a crash occurred. These results can help agencies understand how crowdsourced data can be effectively utilized to best improve freeway operations.
Insect Infestation Increases Viscosity of Biogenic Secondary Organic Aerosol

Plant stress alters emissions of volatile organic compounds. However, little is known about how this could influence climate-relevant properties of secondary organic aerosol (SOA), particularly from complex mixtures such as real plant emissions. In this study, the chemical composition and viscosity were examined for SOA generated from real healthy and aphid-stressed Canary Island pine (Pinus canariensis) trees, which are commonly used for landscaping in Southern California. Healthy Canary Island pine (HCIP) and stressed Canary Island pine (SCIP) aerosols were generated in a 5 m3 environmental chamber at 35–84% relative humidity and room temperature via OH-initiated oxidation. Viscosities of the collected particles were measured using an offline poke-flow method, after conditioning the particles in a humidified air flow. SCIP particles were consistently more viscous than HCIP particles. The largest differences in particle viscosity were observed in particles conditioned at 50% relative humidity where the viscosity of SCIP particles was an order of magnitude larger than that of HCIP particles. The increased viscosity for the aphid-stressed pine tree SOA was attributed to the increased fraction of sesquiterpenes in the emission profile. The real pine SOA particles, both healthy and aphid-stressed, were more viscous than α-pinene SOA particles, demonstrating the limitation of using a single monoterpene as a model compound to predict the physicochemical properties of real biogenic SOA. However, synthetic mixtures composed of only a few major compounds present in emissions (<10 compounds) can reproduce the viscosities of SOA observed from the more complex real plant emissions.
Disinfection of Escherichia coli and Salmonella enterica using the contamination sanitization inspection and disinfection (CSI-D) device

Escherichia coli and Salmonella enterica are significant causes of gastrointestinal disease globally. The Contamination Sanitization Inspection and Disinfection (CSI-D) device is a handheld fluorescence-based imaging system that disinfects food contact surfaces using ultraviolet-C (UVC) illumination. The goal of this study was to determine the optimal parameters for disinfection of E. coli and S. enterica using the CSI-D system. E. coli and S. enterica Enteritidis, Newport, Typhimurium, and Javiana were grown on selective media, followed by transfer to Luria Bertani broth. After overnight incubation, the cultures were diluted and spread-plated on L-agar. The plates were exposed to high-intensity (10 mW/cm2) or low-intensity (5 mW/cm2) UVC for 1 s, 3 s, or 5 s. Exposed and control plates were incubated at room temperature for 2-3 h, then overnight at 37°C. The resulting colonies were counted and compared to control plates. Three trials were conducted on separate days. The average of the trials showed that exposure times of 3-5 s at either intensity resulted in effective and consistent destruction of E. coli and S. enterica. The minimum reduction at 3 s exposure for both intensities was 96%, with a maximum of 100%. The 1 s exposure time showed inconsistent results, with a 0-61.5% survival rate. The results of this study show that exposure to UVC for at least 3 s is required to achieve consistent disinfection of 96-100% for generic E. coli and S. enterica.
Blockchain-Based Access and Timeliness Control for Administrative Punishment Market Supervision

Administrative punishment is one of the most important ways of enforcing administrative law in the field of market supervision in China. However, at the current stage, the abuse of data access permission and the difficulty in managing timeliness in administrative punishment still remain unresolved, which hinders the legalization and standardization of the administrative punishment system. Inspired by blockchain, which is inherently traceable, tamper-proof, and transparent, we design a system, punishment supervisor (PEATS), which is suitable for administrative punishment and technically overcomes the defects of the traditional administrative punishment procedure. To prevent the abuse of data access permission, we innovatively introduce the authorization control gateway (ACG) to verify the access permission of users based on the records in the market supervision department (MSD) contract. To ensure the timeliness of the administrative punishment procedure, we design a special case contract that has the same status as the general case processing state of administrative punishment to track case progress on the blockchain. We experiment and evaluate PEATS in terms of functionality and performance and find that PEATS provides traceability, transparency, and timeliness assurance. In addition, PEATS has 80.9% of the throughput of a traditional server with no more than an additional 3% latency and at most 60 kB additional storage space per case.
The Surface Accelerations Reference—A Large-Scale, Interactive Catalog of Passenger Vehicle Accelerations

There is a need for a large-scale, real world, diverse, and context rich vehicle acceleration catalog that can be used to design, analyze, and compare various intelligent transportation systems. This paper fulfills three primary objectives. First, it provides such a catalog through the Surface Accelerations Reference, which is openly available as an interactive analytics tool as well as an open and downloadable dataset. The Surface Accelerations Reference statistically describes the driving profiles of about 3,500 individuals contributing 34 million miles of continuous driving data collected in the Second Strategic Highway Research Program Naturalistic Driving Study (SHRP 2 NDS). These profiles were created by summarizing billions of longitudinal and lateral acceleration epochs experienced by the participants. Second, this paper introduces a standardized methodology for creating such a catalog so that similar acceleration profiles can be produced for other human cohorts or automated driving systems. Finally, the data are used to analyze the effect of roadway speed category on the rates of lateral and longitudinal acceleration epochs at various thresholds. It is observed that, for the median driver, the rates of epochs are up to three orders of magnitude higher on low-speed roads as compared to high-speed roads. This catalog will facilitate intelligent vehicle system designers to compare and tune their systems for safer driving experiences. It will also allow agencies with similar data to create comparable catalogs facilitating safety and behavioral comparisons between populations.
Non-linear Impacts of Public Debt on Growth, Investment and Credit: A Dynamic Panel Threshold Approach

This paper examines the effects of public debt on the growth rate, investment and domestic credit provided to private sector using the dynamic panel threshold regression method for a large number of developing countries, namely 53 (48) economies for growth and investment (credit) regressions. Our results suggest that public debt does not have a significant impact on the economic growth rate. Despite a strong negative effect of public debt on the total investment, our results do not support the existence of a (strong) threshold effect of public debt on total (private) investment. On the other hand, we present evidence for a threshold effect of public debt on public investment and credit. More precisely, public debt leads to a reduction in public investment and credit when the public debt exceeds the estimated threshold levels. Since public debt matters for investment and credit, it is important to ensure fiscal discipline and prudence in the long term.