syedzayyan/paper_mill_benchmark huggingface dataset:
Exploring the optimal strategy of imputation from SNP array to whole-genome sequencing data in farm animals.

Genotype imputation from bead chip to whole-genome sequencing (wgs) data is a cost-effective method of obtaining genotypes of wgs variants.Beagle, one of the most popular imputation software programs, has been widely used for genotype inference in humans and non-human species.A few studies have systematically and comprehensively compared the performance of beagle versions and parameter settings of farm animals.Here, we investigated the imputation performance of three representative versions of beagle (beagle 4.1, beagle 5.0, and beagle 5.4), and the effective population size (ne) parameter setting for three species (cattle, pig, and chicken).Six scenarios were investigated to explore the impact of certain key factors on imputation performance.The results showed that the default ne (1,000,000) is not suitable for livestock and poultry in small reference or low-density arrays of target panels, with 2.47%-10.45% drops in accuracy.Beagle 5 significantly reduced the computation time (4.66-fold-13.24-fold) without an accuracy loss.In addition, using a large combined-reference panel or high-density chip provides greater imputation accuracy, especially for low minor allele frequency (maf) variants.Finally, a highly significant correlation in the measures of imputation accuracy can be obtained with an maf equal to or greater than 0.05.

Journal: Frontiers in genetics (2022)
Publication types: Journal Article
Acute organoaxial gastric volvulus-A dangerous twist.

Acute gastric volvulus is a rare yet life-threatening condition with mortality ranging from 30% to 50% if not treated promptly.The stomach rotates on itself causing strangulation precipitating necrosis, cameron lesions, and perforation.Long-standing paraesophageal hernia is a common cause of organoaxial gastric volvulus.

Journal: Clinical case reports (2022)
Publication types: Case Reports;Journal Article
A Single Vaccine Protects against SARS-CoV-2 and Influenza Virus in Mice.

The ongoing sars-co v-2 pandemic poses a severe global threat to public health, as do influenza viruses and other coronaviruses.Here, we present chimpanzee adenovirus 68 (ad c68)-based vaccines designed to universally target coronaviruses and influenza.Our design is centered on an immunogen generated by fusing the sars-co v-2 receptor-binding domain (rbd) to the conserved stalk of h7n9 hemagglutinin (ha).Remarkably, the constructed vaccine effectively induced both sars-co v-2-targeting antibodies and anti-influenza antibodies in mice, consequently affording protection from lethal sars-co v-2 and h7n9 challenges as well as effective h3n2 control.We propose our ad c68-vectored coronavirus-influenza vaccine as a universal approach toward curbing respiratory virus-causing pandemics.importancethe covid-19 pandemic exemplifies the severe public health threats of respiratory virus infection and influenza a viruses.The currently envisioned strategy for the prevention of respiratory virus-causing diseases requires the comprehensive administration of vaccines tailored for individual viruses.Here, we present an alternative strategy by designing chimpanzee adenovirus 68-based vaccines which target both the sars-co v-2 receptor-binding-domain and the conserved stalk of influenza hemagglutinin.When tested in mice, this strategy attained potent neutralizing antibodies against wild-type sars-co v-2 and its emerging variants, enabling an effective protection against lethal sars-co v-2 challenge.Notably, it also provided complete protection from lethal h7n9 challenge and efficient control of h3n2-induced morbidity.Our study opens a new avenue to universally curb respiratory virus infection by vaccination.

Journal: Journal of virology (2022)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
A New Water Level Measurement Method Combining Infrared Sensors and Floats for Applications on Laboratory Scale Channel under Unsteady Flow Regime.

In this paper, we studied water transport under an unsteady flow regime in an experimental channel (4 m in length; 3 cm in width).Our experiments implicated some measuring requirements, specifically, a water level (wl) detection technique that is able to measure wl in a range of 2 cm with a precision of 1 mm.The existing wl detection techniques could not meet our measurement requirements.Therefore, we propose a new measurement method that combines two approaches: an "old" water contact technique (float) with a "new" remote non-contact technique (infrared sensor).We used an extruded polystyrene (xps foam) that needed some adequate treatment before using it as float in experimental measurements.The combination of ir-sensors with treated float foam lead to a sensitive measurement method that is able to detect flat and sharp flow signals, as well as highly dynamic variations of water surface level.Based on the experimental measurements of wl and outflow at the channel output, we deduced a loop rating curve that is suitable with a power law adjustment.The new measurement method could be extended to larger scale applications like rivers and more complicated cross section geometry of irregular shape.

Journal: Sensors (Basel, Switzerland) (2019)
Publication types: Journal Article
Adipose Tissue Uses in Peripheral Nerve Surgery.

Currently, many different techniques exist for the surgical repair of peripheral nerves.The degree of injury dictates the repair and, depending on the defect or injury of the peripheral nerve, plastic surgeons can perform nerve repairs, grafts, and transfers.All the previously listed techniques are routinely performed in human patients, but a novel addition to these peripheral nerve surgeries involves concomitant fat grafting to the repair site at the time of surgery.Fat grafting provides adipose-derived stem cells to the injury site.Though fat grafting is performed as an adjunct to some peripheral nerve surgeries, there is no clear evidence as to which procedures have improved outcomes resultant from concomitant fat grafting.This review explores the evidence presented in various animal studies regarding outcomes of fat grafting at the time of various types of peripheral nerve surgery.

Journal: International journal of molecular sciences (2022)
Publication types: Journal Article;Review
Multimodal imaging of an idiopathic florid vascularised epiretinal membrane: Course, treatment, and outcome.

Idiopathic vascular epiretinal membrane is an extremely rare entity and the pathogenesis and clinical course is not clearly understood.A 53-year-old hypertensive female patient presented with complaints of altered vision in the right eye.On examination, her vision was 20/30 and fundoscopy showed a vascularized epiretinal membrane (erm), which was confirmed on spectral-domain optical coherence tomography.No primary cause was found after investigations.The symptoms and erm showed slow progression over the next three years with a visual acuity of 20/60.She underwent surgery for removal of the erm, which was subjected to histopathological evaluation.This is a unique case of a florid proliferative vascularisation of an erm in the absence of any identifiable cause, which had a good visual outcome following surgery.

Journal: Indian journal of ophthalmology (2020)
Publication types: Case Reports;Journal Article
Visual Working Memory Adapts to the Nature of Anticipated Interference.

Visual working memory has been proven to be relatively robust against interference.However, little is known on whether such robust coding is obligatory, or can be flexibly recruited depending on its expected usefulness.To address this, participants remembered both the color and orientation of a grating.During the maintenance, we inserted a secondary color/orientation memory task, interfering with the primary task.Crucially, we varied the expectations of the type of interference by varying the probability of the two types of intervening task.Behavioral data indicate that to-be-remembered features for which interference is expected are bolstered, whereas to-be-remembered features for which no interference is expected are left vulnerable.This was further supported by f mri data obtained from visual cortex.In conclusion, the flexibility of visual working memory allows it to strengthen memories for which it anticipates the highest risk of interference.

Journal: Journal of cognitive neuroscience (2022)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Inflammation and Oxidative Stress in Seminal Plasma: Search for Biomarkers in Diagnostic Approach to Male Infertility.

Oxidative and inflammatory damage underlie several conditions related to male infertility, including varicocele.Free light chains of immunoglobulins (flcs) are considered markers of low-grade inflammation in numerous diseases.Coenzyme q10 (co q10), a lipidic antioxidant and anti-inflammatory compound, is involved in spermatozoa energy metabolism and motility.We aimed to evaluate flcs' seminal levels in patients with varicocele in comparison to control subjects and to correlate them with co q10 and total antioxidant capacity (tac) in human semen.Sixty-five patients were enrolled.Semen analysis was performed; patients were divided into three groups: controls, 12 normozoospermic patients, aged 34 (33-41) years; varicocele (var), 29 patients, aged 33 (26-37) years; and idiopathic, 24 oligo-, astheno- and oligoasthenozoospermic patients aged 37 (33.5-40.5) years.Flcs (κ and λ) were assayed by turbidimetric method; co q10 by hplc; tac by spectrophotometric method.Λ flcs showed a trend toward higher levels in var vs.Controls and the idiopathic group.Var showed a trend toward lower κ flcs levels vs.The other two groups.When comparing κ/λ ratio, var showed significantly lower levels vs.Controls and idiopathic.Moreover, co q10 seminal levels showed higher levels in var and idiopathic compared to controls.Data reported here confirm lower levels of κ/λ ratio in var and suggest a possible application in personalized medicine as clinical biomarkers for male infertility.

Journal: Journal of personalized medicine (2022)
Publication types: Journal Article
Correlating ligand-to-metal charge transfer with voltage hysteresis in a Li-rich rock-salt compound exhibiting anionic redox.

Anionic redox is a double-edged sword for li-ion cathodes because it offers a transformational increase in energy density that is also negated by several detrimental drawbacks to its practical implementation.Among them, voltage hysteresis is the most troublesome because its origin is still unclear and under debate.Herein, we tackle this issue by designing a prototypical li-rich cation-disordered rock-salt compound li1.17ti0.33fe0.5o2that shows anionic redox activity and exceptionally large voltage hysteresis while exhibiting a partially reversible fe migration between octahedral and tetrahedral sites.Through combined in situ and ex situ spectroscopic techniques, we demonstrate the existence of a non-equilibrium (adiabatic) redox pathway enlisting fe3+/fe4+and o redox as opposed to the equilibrium (non-adiabatic) redox pathway involving sole o redox.We further show that the charge transfer from o(2p) lone pair states to fe(3d) states involving sluggish structural distortion is responsible for voltage hysteresis.This study provides a general understanding of various voltage hysteresis signatures in the large family of li-rich rock-salt compounds.

Journal: Nature chemistry (2021)
Publication types: Journal Article
Outcome of pregnancies with first-trimester increased nuchal translucency and cystic hygroma in a tertiary maternity hospital in United Arab Emirates.

To study the outcome of pregnancies with first-trimester increased nuchal translucency and cystic hygromas.Methodology retrospective study of 132 pregnancies with first-trimester increased nuchal translucency and cystic hygromas, between january 2015 to december 2018 at corniche hospital, abu dhabi, uae.Fetal karyotyping, detailed ultrasound at 18-22 weeks and fetal echocardiography were offered to all women.Adverse outcomes included miscarriage, intrauterine fetal death, termination of pregnancy, neonatal death and structural abnormalities.Results of the 132 pregnancies, 13 had nt > 95th percentile, 89 had nt ≥3 mm and 30 had cystic hygroma.Among 13 pregnancies with nt > 95th centile, 7.6% had abnormal karyotype.Among 89 pregnancies with nt ≥3 mm, 29.2% had abnormal karyotype, 13.4% miscarriage, 7.8% underwent top, 5.6% intrauterine fetal death, 1.1% neonatal death and 14.6% had structural abnormalities.Among 30 pregnancies with cystic hygroma, 40% had abnormal karyotype, 20% miscarriage, 13.3% top, 13.3% intrauterine fetal death, 6.6% had neonatal death and 20% had structural abnormalities.Conclusion in our study, karyotype abnormalities increased with increasing nuchal translucency with highest risk in fetuses with cystic hygromas.Increased nuchal translucency was associated with adverse pregnancy outcome, which was higher in the group with nt≥6 mm and cystic hygromas.

Journal: International journal of gynaecology and obstetrics: the official organ of the International Federation of Gynaecology and Obstetrics (2022)
Publication types: Journal Article
Learning from the GP-consultant exchange scheme: a qualitative evaluation.

Collaborative working across primary and secondary care is crucial to providing high quality patient care.There is still a lack of communication and understanding between primary and secondary care, which can impede collaborative working.The experience of observing colleagues in a different speciality can prompt insight, improve morale and promote collaborative working.The gp-consultant exchange scheme aimed to improve professional understanding, foster deeper partnerships, and ignite opportunities for innovation and/or quality improvement (qi) with co-owned local solutions.This paper gives an overview of how the scheme works and sets out some of the outcomes reported by some 200 consultants and gps participants to date.Overall, the participants found the scheme an enjoyable way to reconnect clinicians and allowed them to learn about the challenges faced in different areas within the nhs.This low-cost intervention needs motivated individuals to drive the project forward and make it sustainable, but it can be replicated within any organisation or profession in the nhs.

Journal: MedEdPublish (2016) (2022)
Publication types: Case Reports;Journal Article
Odd-Even Effect on Supramolecular Co-Assemblies: Control over the Two-Dimensional Self-Assemblies of a Fluorenone Derivative with Asymmetrically Substituted Alkyl Chains.

The precise control of two-dimensional supramolecular co-assemblies presents a research topic related to advance nanotechnology.Here, we report a scanning tunneling microscopy (stm) study of the mixture behavior of three fluorenone derivatives at the liquid-solid interface.The target molecule is f-c12c13whose structure bears asymmetrical alkyls, whereas the regulating molecules, either f-c12c12or f-c13c13, are structurally symmetric.By stm imaging of systematic mixtures with various volumes among the sample solutions, we found that the mixing ratio mainly determined the binary outcomes.Compared with f-c12c12, f-c13c13shows a stronger ability to dominate the patterning, explained by the larger binding and adsorption energies calculated by the force field simulations.Moreover, the odd-even effect exists in the system.Overall, we acquired knowledge about the regulating ability of bi-component supramolecular assembling, especially for structurally asymmetric molecular systems.

Journal: Langmuir : the ACS journal of surfaces and colloids (2022)
Publication types: Journal Article
Tropical extreme droughts drive long-term increase in atmospheric CO2growth rate variability.

The terrestrial carbon sink slows the accumulation of carbon dioxide (co2) in the atmosphere by absorbing roughly 30% of anthropogenic co2emissions, but varies greatly from year to year.The resulting variations in the atmospheric co2growth rate (cgr) have been related to tropical temperature and water availability.The apparent sensitivity of cgr to tropical temperature ([formula: see text]) has changed markedly over the past six decades, however, the drivers of the observation to date remains unidentified.Here, we use atmospheric observations, multiple global vegetation models and machine learning products to analyze the cause of the sensitivity change.We found that a threefold increase in [formula: see text] emerged due to the long-term changes in the magnitude of cgr variability (i.e., indicated by one standard deviation of cgr; stdcgr), which increased 34.7% from 1960-1979 to 1985-2004 and subsequently decreased 14.4% in 1997-2016.We found a close relationship (r2= 0.75, p < 0.01) between stdcgrand the tropical vegetated area (23°s - 23°n) affected by extreme droughts, which influenced 6-9% of the tropical vegetated surface.A 1% increase in the tropical area affected by extreme droughts led to about 0.14 pg c yr-1increase in stdcgr.The historical changes in stdcgrwere dominated by extreme drought-affected areas in tropical africa and asia, and semi-arid ecosystems.The outsized influence of extreme droughts over a small fraction of vegetated surface amplified the interannual variability in cgr and explained the observed long-term dynamics of [formula: see text].

Journal: Nature communications (2022)
Publication types: Journal Article;Research Support, Non-U.S. Gov't;Research Support, U.S. Gov't, Non-P.H.S.
Oligosaccharide mapping analysis by HILIC-ESI-HCD-MS/MS for structural elucidation of fucoidan from sea cucumber Holothuria floridana.

The elucidation of precise structure of fucoidan is essential for understanding their structure-function relationship and promoting the development of marine drugs.In this work, we firstly reported the oligosaccharide mapping of fucoidan from holothuria floridana using a combination of hydrothermal depolymerization, hydrophilic interaction liquid chromatography (hilic) coupled with electrospray mass spectrometry (esi-ftms) and high energy collision-induced dissociation (hcd-ms/ms) and 2d nmr analysis.With careful selection of fully deprotonated molecular ions of fucoidan oligosaccharides and their na bd4reduced alditols, hilic-esi-hcd-ms/ms provided structurally relevant glycosidic product ions with no sulfate loss for definitive assignment of sequence and sulfation pattern of all the oligosaccharides and their isomers from dp2 to dp7 from hydrothermal depolymerization.The oligosaccharide mapping clarified the structure of fucoidan with various oligosaccharide domains with 2,4-di-o-sulfated and 2-o sulfated fucose residues.

Journal: Carbohydrate polymers (2022)
Publication types: Journal Article
Simulation and Optimization of CNTs Cold Cathode Emission Grid Structure.

Carbon nanotubes (cnts) show significant advantages in the development of cold cathode x-ray tubes due to their excellent field emission performance; however, there are still some problems, such as short lifetime and the low emission current of large-area cnts.In this paper, a front-grid carbon nanotube array model was established, and the electric field intensity near the tip of the cnts' electric field enhancement factor was analytically calculated.A simulation model of a cnt three-dimensional field emission electron gun was established by using computer simulation technology (cst).The effects of grid wire diameter, grid aperture shape, and the distribution of grid projection on the cathode surface on the cathode current, anode current, and electron transmission efficiency were analyzed.The aperture ratio was used to evaluate the grid performance, and the simulation results show that the ideal aperture ratio should be between 65% and 85%.A grid structure combining a coarse grid and a fine grid was designed, which can make the electric field intensity around the grid evenly distributed, and effectively increased the cathode emission current by 24.2% compared with the structure without the fine grid.The effect of grid aperture ratio on the electron transmission efficiency was tested.The simulation results and optimized structure can provide a reference for the grid design of cold cathode emission x-ray tubes.

Journal: Nanomaterials (Basel, Switzerland) (2022)
Publication types: Journal Article
Sweep Jet Collection Laser-Induced Acoustic Desorption Atmospheric Pressure Photoionization for Lipid Analysis Applications.

Laser-induced acoustic desorption coupled to microplasma-based atmospheric pressure photoionization (liad-appi) using a nebulized sweep jet to aid in dopant introduction and ion transmission has been applied to the analysis of model, apolar lipid compounds.Specifically, several sterols, sterol esters, and triacylglycerols were detected using dopants such as anisole and toluene.Additionally, several triacylglycerols, sterols, carboxylic acids, and hopanoids were detected from complex mixtures of olive oil and australian shale rock extract as a first demonstration of the applicability of liad-appi on real-world samples.Detection limits using a sweep jet configuration for α-tocopherol and cholesterol were found to be 609 ± 61 and 292 ± 29 fmol, respectively.For sterol esters and triacylglycerols with a large number of double bonds in the fatty acid chain, liad-appi was shown to yield greater molecular ion or [m+nh4]+abundances than those with saturated fatty acid chains.Dopants such as anisole and toluene, with ionization potentials (ips) of 8.2 and 8.8 e v, respectively, were tested.A greater degree of fragmentation with several of the more labile test compounds was observed using toluene.Overall, liad-appi with a nebulized sweep jet requires minimal sample preparation and is a generally useful and sensitive analysis technique for low-polarity mixtures of relevance to biochemical assays and geochemical profiling.Graphical abstract.

Journal: Journal of the American Society for Mass Spectrometry (2019)
Publication types: Journal Article
Treatment of Central Nervous System Infection Caused by Multidrug-ResistantKlebsiella pneumoniaewith Colistin Sulfate Intravenously and Intrathecally: A Case Report.

Due to the blood-brain barrier and limited antibiotic choices, polymyxin is currently the first-line agent for the treatment of central nervous system infections (cnsis) caused by multidrug-resistant gram-negative bacteria (mdr-gnb).Colistin sulfate, as a polymyxin e different from cms, is used in chinese clinics, and there are limited reports on its use in the treatment of cnsis.case presentation:this case describes a 76-year-old man who underwent complex neurosurgery for cervical spinal stenosis.Postoperatively, the patient developed a fever and a poorly healed surgical wound.Numerous blood routine tests, inflammatory markers, pathogenic tests of cervical secretions, cerebrospinal fluid (csf), and sputum were sent for diagnosis.After empirical antimicrobial treatments failed, the csf and wound pus cultured carbapenem-resistant klebsiella pneumoniae.The regimen was adjusted to colistin sulfate intravenously and intrathecal injection combined with tigecycline.In addition, the management of infection foci, including continuous lumbar pool drain, cervical 3-5 internal fixation removal with cervical 1-6 spine dilation, csf leak repair, and right thigh broad fasciotomy, were performed.After treatment, the patient was discharged with multiple sets of negative csf cultures and the infection under control.conclusions:for cnsis caused by mdr-gnb, the selection of colistin sulfate for intravenous and topical combination treatment is a viable choice.

Journal: Pharmaceuticals (Basel, Switzerland) (2022)
Publication types: Case Reports;Journal Article