Miracle-dz/UniFAR-FTUs huggingface dataset:
Typical Males and Unconventional Females: Songs and Singing Behaviors of a Tropical, Duetting Oriole in the Breeding and Non-Breeding Season

Recent research emphasizes that female song is evolutionarily important, yet there are still few species for which we have quantified the similarities and differences between male and female song. Comparing song rates and the structure of female and male song is an important first step to forming hypotheses about functional and evolutionary differences that may exist between females and males, especially in year-round territorial species that may use their songs for breeding and non-breeding activities. We compared female and male singing rates and song structure in a tropical New World oriole, the Venezuelan troupial (Icterus icterus) during both the breeding and non-breeding season and between the dawn and day. Males sang solos at particularly high rates during the breeding season before dawn. Females, however, sang at consistent rates year-round, primarily during the day. Females answered 75% of male day songs, producing duets, whereas males overlapped only 42% of female songs. Duets were common year-round, but occurred more often during the non-breeding season. Structurally, female songs were higher pitched and shorter than male songs. We detected no sex differences in the number or order of syllables, however, interestingly, answers were shorter than duet initiations and solos, and, during the breeding season, songs that initiated duets were characterized by higher syllable diversity than were answers or solos. The fact that males sing more during the breeding season supports the classical hypothesis that male song is a sexually selected trait. However, our findings that females sing solos and answer the majority of male songs to create duets year-round suggests that female song may have evolved to serve multiple functions not exclusively tied to breeding.
Fishing for causes and cures of motor neuron disorders

Motor neuron disorders (MNDs) are a clinically heterogeneous group of neurological diseases characterized by progressive degeneration of motor neurons, and share some common pathological pathways. Despite remarkable advances in our understanding of these diseases, no curative treatment for MNDs exists. To better understand the pathogenesis of MNDs and to help develop new treatments, the establishment of animal models that can be studied efficiently and thoroughly is paramount. The zebrafish (Danio rerio) is increasingly becoming a valuable model for studying human diseases and in screening for potential therapeutics. In this Review, we highlight recent progress in using zebrafish to study the pathology of the most common MNDs: spinal muscular atrophy (SMA), amyotrophic lateral sclerosis (ALS) and hereditary spastic paraplegia (HSP). These studies indicate the power of zebrafish as a model to study the consequences of disease-related genes, because zebrafish homologues of human genes have conserved functions with respect to the aetiology of MNDs. Zebrafish also complement other animal models for the study of pathological mechanisms of MNDs and are particularly advantageous for the screening of compounds with therapeutic potential. We present an overview of their potential usefulness in MND drug discovery, which is just beginning and holds much promise for future therapeutic development.
Flexible Pressure Sensor with Ag Wrinkled Electrodes Based on PDMS Substrate

Flexible pressure sensors are essential components of electronic skins for future attractive applications ranging from human healthcare monitoring to biomedical diagnostics, robotic skins, and prosthetic limbs. Here we report a new kind of flexible pressure sensor. The sensors are capacitive, and composed of two Ag wrinkled electrodes separated by a carbon nanotubes (CNTs)/polydimethylsiloxane (PDMS) composite deformable dielectric layer. Ag wrinkled electrodes were formed by vacuum deposition on top of pre-strained and relaxed PDMS substrates which were treated using an O2 plasma, a surface functionalization process, and a magnetron sputtering process. Ultimately, the developed sensor exhibits a maximum sensitivity of 19.80% kPa−1 to capacitance, great durability over 500 cycles, and rapid mechanical responses (<200 ms). We also demonstrate that our sensor can be used to effectively detect the location and distribution of finger pressure.
What distributional information is useful and usable for language acquisition

Numerous theories of language acquisition have indicated that distributional information is extremely valuable for assisting the child to learn syntactic categories, yet these theories differ over the type of information that is proposed as useful in acquisition. Mintz (2003) has proposed that children utilize the previous word and the following word (AxB frames) for acquiring categories, whereas Monaghan, Chater, and Christiansen (submitted) have suggested that information about the previous word alone provides a rich source of data for categorization. In three modeling experiments we found that bigrams were better than fixed AxB frames for learning syntactic categories in a corpus of child-directed speech. However, presentation of the preceding and succeeding words when these can be processed separately resulted in better learning than presenting the preceding word alone, and also improved performance over presenting the previous two words.
Effect of Windrow Management on Ammonia and Nitrous Oxide Emissions from Swine Manure Composting

: In the era of sustainability, utilization of livestock wastes as soil amendment to provide micronutrients for crops is very economical and sustainable. It is well understood that livestock wastes are comparable, if not better, nutrient sources for crops as chemical fertilizers. However, the large concentrated volumes of animal manure produced from livestock operations and the limited amount of available nearby agricultural land areas necessitated the need for volume reduction of these animal wastes. Composting of these animal manures is a viable option for biomass and pathogenic reduction in the environment. Nevertheless, composting also increases the potential loss of available nutrients for crop production as well as unwanted emission of anthropogenic air pollutants due to the loss of ammonia and other compounds via volatilization. In this study, we examine the emission of ammonia and nitrous oxide from swine manure windrows to evaluate the benefit of biomass reduction in conjunction with the potential loss of available nutrients. The feedstock for the windrows was obtained from swine farm in Kentucky where swine manure was mixed with wood shaving as absorbent material. Static flux chambers along with photoacoustic gas analyzer were used to monitor ammonia and nitrous oxide concentrations during the composting process. The results show that ammonia and nitrous oxide fluxes were quite high during the initial composting process and after the turning of each compost pile. Over the period of roughly three months of composting, the biochemical oxygen demand (BOD) decreased by about 90%. Although composting of animal waste is quite beneficial for biomass reduction, composting may not be economically feasible from an agronomical point of view due to time, nutrient loss (N loss), and potential environmental pollution (ammonia and greenhouse gas emissions). Therefore, additional studies are needed to assess and validate the economics and environmental impact of animal (swine) manure composting (e.g., crop yield or impact on climate change).
Nation-Based Occurrence and Endogenous Biological Reduction of Mycotoxins in Medicinal Herbs and Spices

Medicinal herbs have been increasingly used for therapeutic purposes against a diverse range of human diseases worldwide. Moreover, the health benefits of spices have been extensively recognized in recent studies. However, inevitable contaminants, including mycotoxins, in medicinal herbs and spices can cause serious problems for humans in spite of their health benefits. Along with the different nation-based occurrences of mycotoxins, the ultimate exposure and toxicities can be diversely influenced by the endogenous food components in different commodities of the medicinal herbs and spices. The phytochemicals in these food stuffs can influence mold growth, mycotoxin production and biological action of the mycotoxins in exposed crops, as well as in animal and human bodies. The present review focuses on the occurrence of mycotoxins in medicinal herbs and spices and the biological interaction between mold, mycotoxin and herbal components. These networks will provide insights into the methods of mycotoxin reduction and toxicological risk assessment of mycotoxin-contaminated medicinal food components in the environment and biological organisms.
Paleoproductivity Reconstructions for the Paleogene Southern Ocean: A Direct Comparison of Geochemical and Micropaleontological Proxies

The reliability of paleoproductivity proxies must be determined before assessing the role of the oceanic carbon (C) cycle in affecting past climate changes. We compare paleoproductivity records of newly generated micropaleontological data (benthic foraminiferal accumulation rates, BFAR) to those of existing geochemical data (reactive phosphorus [reactive P] mass accumulation rates [MAR] and biological barium [bio‐Ba] MAR) for the same Paleogene‐aged sediments. Sediments are from the Atlantic (Maud Rise, Ocean Drilling Program Sites 689/690) and the Indian (Kerguelen plateau, Ocean Drilling Program Site 738) sectors of the Southern Ocean. Reactive P MAR, but not bio‐Ba MAR, correlates to varying degree with BFAR for all three sites investigated. Export productivity, delivery of organic C to the seafloor, and organic C burial calculated here using bio‐Ba MAR, BFAR, and reactive P MAR, respectively, for these sites during the Early Paleogene span 2 orders of magnitude (~0.01 to 1 g C·cm−2·kyr−1). Differences in magnitude of reconstructed organic C fluxes are expected because different proxies record different aspects of the biological pump, and these aspects did not behave proportionally similar for all periods. Proxies studied here indicate that transfer efficiency, the fraction of exported organic matter from 100 m that reaches the deep ocean, was low for the Early Paleogene Southern Ocean, similar to today. Despite this, absolute organic carbon burial was similar or higher than today because export productivity was similar or higher. Elevated temperatures may have increased both biological production and respiration in the Early Paleogene Southern Ocean.
Systemic HMGB1 Neutralization Prevents Postoperative Neurocognitive Dysfunction in Aged Rats

Postoperative neurocognitive disorders are common complications in elderly patients following surgery or critical illness. High mobility group box 1 protein (HMGB1) is rapidly released after tissue trauma and critically involved in response to sterile injury. Herein, we assessed the role of HMGB1 after liver surgery in aged rats and explored the therapeutic potential of a neutralizing anti-HMGB1 monoclonal antibody in a clinically relevant model of postoperative neurocognitive disorders. Nineteen to twenty-two months Sprague-Dawley rats were randomly assigned as: (1) control with saline; (2) surgery, a partial hepatolobectomy under sevoflurane anesthesia and analgesia, + immunoglobulin G as control antibody; (3) surgery + anti-HMGB1. A separate cohort of animals was used to detect His-tagged HMGB1 in the brain. Systemic anti-HMGB1 antibody treatment exerted neuroprotective effects preventing postoperative memory deficits and anxiety in aged rats by preventing surgery-induced reduction of phosphorylated cyclic AMP response element-binding protein in the hippocampus. Although no evident changes in the intracellular distribution of HMGB1 in hippocampal cells were noted after surgery, HMGB1 levels were elevated on day 3 in rat plasma samples. Experiments with tagged HMGB1 further revealed a critical role of systemic HMGB1 to enable an access to the brain and causing microglial activation. Overall, these data demonstrate a pivotal role for systemic HMGB1 in mediating postoperative neuroinflammation. This may have direct implications for common postoperative complications like delirium and postoperative cognitive dysfunction.
Genetic Determinants of Long-Term Changes in Blood Lipid Concentrations: 10-Year Follow-Up of the GLACIER Study

Recent genome-wide meta-analyses identified 157 loci associated with cross-sectional lipid traits. Here we tested whether these loci associate (singly and in trait-specific genetic risk scores [GRS]) with longitudinal changes in total cholesterol (TC) and triglyceride (TG) levels in a population-based prospective cohort from Northern Sweden (the GLACIER Study). We sought replication in a southern Swedish cohort (the MDC Study; N = 2,943). GLACIER Study participants (N = 6,064) were genotyped with the MetaboChip array. Up to 3,495 participants had 10-yr follow-up data available in the GLACIER Study. The TC- and TG-specific GRSs were strongly associated with change in lipid levels (β = 0.02 mmol/l per effect allele per decade follow-up, P = 2.0×10−11 for TC; β = 0.02 mmol/l per effect allele per decade follow-up, P = 5.0×10−5 for TG). In individual SNP analysis, one TC locus, apolipoprotein E (APOE) rs4420638 (β = 0.12 mmol/l per effect allele per decade follow-up, P = 2.0×10−5), and two TG loci, tribbles pseudokinase 1 (TRIB1) rs2954029 (β = 0.09 mmol/l per effect allele per decade follow-up, P = 5.1×10−4) and apolipoprotein A-I (APOA1) rs6589564 (β = 0.31 mmol/l per effect allele per decade follow-up, P = 1.4×10−8), remained significantly associated with longitudinal changes for the respective traits after correction for multiple testing. An additional 12 loci were nominally associated with TC or TG changes. In replication analyses, the APOE rs4420638, TRIB1 rs2954029, and APOA1 rs6589564 associations were confirmed (P≤0.001). In summary, trait-specific GRSs are robustly associated with 10-yr changes in lipid levels and three individual SNPs were strongly associated with 10-yr changes in lipid levels.
Paper 2: EUROCAT public health indicators for congenital anomalies in Europe.

OBJECTIVE The purpose of this article is to present the specific public health indicators recently developed by EUROCAT that aim to summarize important aspects of the public health impact of congenital anomalies in a few quantitative measures. METHODS The six indicators are: (1) congenital anomaly perinatal mortality, (2) congenital anomaly prenatal diagnosis prevalence, (3) congenital anomaly termination of pregnancy, (4) Down syndrome livebirth prevalence, (5) congenital anomaly pediatric surgery, and (6) neural tube defects (NTD) total prevalence. Data presented for this report pertained to all cases (livebirths, fetal deaths, or stillbirths after 20 weeks of gestation and terminations of pregnancy for fetal anomaly [TOPFA]) of congenital anomaly from 27 full member registries of EUROCAT that could provide data for at least 3 years during the period 2004 to 2008. Prevalence of anomalies, prenatal diagnosis, TOPFA, pediatric surgery, and perinatal mortality were calculated per 1000 births. RESULTS The overall perinatal mortality was approximately 1.0 per 1000 births for EUROCAT registries with almost half due to fetal and the other half due to first week deaths. There were wide variations in perinatal mortality across the registries with the highest rates observed in Dublin and Malta, registries in countries where TOPFA are illegal, and in Ukraine. The overall perinatal mortality across EUROCAT registries slightly decreased between 2004 and 2008 due to a decrease in first week deaths. The prevalence of TOPFA was fairly stable at about 4 per 1000 births. There were variations in livebirth prevalence of cases typically requiring surgery across the registries; however, for most registries this prevalence was between 3 and 5 per 1000 births. Prevalence of NTD decreased by about 10% from 1.05 in 2004 to 0.94 per 1000 in 2008. CONCLUSION It is hoped that by publishing the data on EUROCAT indicators, the public health importance of congenital anomalies can be clearly summarized to policy makers, the need for accurate data from registries emphasized, the need for primary prevention and treatment services highlighted, and the impact of current services measured.
Dynamics of the base of ribosomal A-site finger revealed by molecular dynamics simulations and Cryo-EM

Helix 38 (H38) of the large ribosomal subunit, with a length of 110 Å, reaches the small subunit through intersubunit bridge B1a. Previous cryo-EM studies revealed that the tip of H38 moves by more than 10 Å from the non-ratcheted to the ratcheted state of the ribosome while mutational studies implicated a key role of flexible H38 in attenuation of translocation and in dynamical signaling between ribosomal functional centers. We investigate a region including the elbow-shaped kink-turn (Kt-38) in the Haloarcula marismortui archaeal ribosome, and equivalently positioned elbows in three eubacterial species, located at the H38 base. We performed explicit solvent molecular dynamics simulations on the H38 elbows in all four species. They are formed by at first sight unrelated sequences resulting in diverse base interactions but built with the same overall topology, as shown by X-ray crystallography. The elbows display similar fluctuations and intrinsic flexibilities in simulations indicating that the eubacterial H38 elbows are structural and dynamical analogs of archaeal Kt-38. We suggest that this structural element plays a pivotal role in the large motions of H38 and may act as fulcrum for the abovementioned tip motion. The directional flexibility inferred from simulations correlates well with the cryo-EM results.
Ultraaccurate genome sequencing and haplotyping of single human cells

Significance Accurate sequencing and haplotyping of diploid genomes of single cells are intrinsically difficult due to the small amount of starting materials and limited read lengths of current DNA sequencing methods. In SISSOR (single-stranded sequencing using microfluidic reactors), we aim to improve sequencing accuracy and haplotype assembly by taking advantage of the redundant complementary sequence information in the double-stranded DNA and by partitioning megabase-size single-stranded DNA fragments from the homologous chromosome pairs into multiple compartments for amplification by MDA (multiple displacement amplification) and subsequent sequencing using short-read DNA sequencing platforms. We report the demonstration of the most accurate single-cell genome sequencing to date with data from three single human cells. Our approach can simultaneously provide higher accuracy and longer haplotypes than existing approaches. Accurate detection of variants and long-range haplotypes in genomes of single human cells remains very challenging. Common approaches require extensive in vitro amplification of genomes of individual cells using DNA polymerases and high-throughput short-read DNA sequencing. These approaches have two notable drawbacks. First, polymerase replication errors could generate tens of thousands of false-positive calls per genome. Second, relatively short sequence reads contain little to no haplotype information. Here we report a method, which is dubbed SISSOR (single-stranded sequencing using microfluidic reactors), for accurate single-cell genome sequencing and haplotyping. A microfluidic processor is used to separate the Watson and Crick strands of the double-stranded chromosomal DNA in a single cell and to randomly partition megabase-size DNA strands into multiple nanoliter compartments for amplification and construction of barcoded libraries for sequencing. The separation and partitioning of large single-stranded DNA fragments of the homologous chromosome pairs allows for the independent sequencing of each of the complementary and homologous strands. This enables the assembly of long haplotypes and reduction of sequence errors by using the redundant sequence information and haplotype-based error removal. We demonstrated the ability to sequence single-cell genomes with error rates as low as 10−8 and average 500-kb-long DNA fragments that can be assembled into haplotype contigs with N50 greater than 7 Mb. The performance could be further improved with more uniform amplification and more accurate sequence alignment. The ability to obtain accurate genome sequences and haplotype information from single cells will enable applications of genome sequencing for diverse clinical needs.
Impact of Rivastigmine Patch and Capsules on Activities of Daily Living in Alzheimer’s Disease

Background: Rivastigmine patches provide similar efficacy to rivastigmine capsules with a lower incidence of gastrointestinal side effects in patients with probable Alzheimer’s disease (AD). Methods: Post hoc analysis of a 24-week, prospective, international, randomized, double-blind, placebo- and active-controlled trial. Patients (n = 892) with probable AD received rivastigmine transdermal patches (9.5 mg/24 hours [10 cm2]), rivastigmine capsules (6 mg twice daily), or placebo, and impact on activities of daily living (ADLs) was assessed utilizing 3 subscales: basic, high-level function, and autonomy. Results: At week 24, both rivastigmine groups demonstrated significantly superior performance in Alzheimer’s Disease Cooperative Study—Activities of Daily Living (ADCS-ADL) Total Score versus placebo (rivastigmine patch, P = .013; capsules, P = .039). Overall, both rivastigmine formulations provided benefits in ADL subscales. For basic ADLs, rivastigmine capsules performed significantly better than placebo (P = .012). For high-level function ADLs, rivastigmine patch performed better than placebo (P = .056). For autonomy ADLs, rivastigmine patch performed significantly better than placebo (P = .017). Conclusion: Rivastigmine patches and capsules provide significant effects in both total and subscale ADLs in patients with probable AD.
Gaming on the Rift: How Virtual Reality Affects Game User Satisfaction

Virtual reality (VR) headsets like the Oculus Rift, HTC Vive, and PlayStation VR can provide a unique experience different from traditional computer monitors. Research demonstrates some support for VR resulting in more immersive gaming than traditional games using a computer or TV monitor. This study investigates how VR technology impacts game user satisfaction. Participants played the same strategy video game using the Oculus Rift, a VR headset, and a computer monitor. Game user satisfaction was measured by the psychometrically validated Game User Experience Satisfaction Scale (GUESS) which consists of nine constructs. Results from this study showed that VR enhanced overall satisfaction, enjoyment, engrossment, creativity, sound, and graphics quality.