syedzayyan/paper_mill_benchmark huggingface dataset:
Optimal Bayesian supervised domain adaptation for RNA sequencing data.

Motivation when learning to subtype complex disease based on next-generation sequencing data, the amount of available data is often limited.Recent works have tried to leverage data from other domains to design better predictors in the target domain of interest with varying degrees of success.But they are either limited to the cases requiring the outcome label correspondence across domains or cannot leverage the label information at all.Moreover, the existing methods cannot usually benefit from other information available a priori such as gene interaction networks.Results in this article, we develop a generative optimal bayesian supervised domain adaptation (obsda) model that can integrate rna sequencing (rna-seq) data from different domains along with their labels for improving prediction accuracy in the target domain.Our model can be applied in cases where different domains share the same labels or have different ones.Obsda is based on a hierarchical bayesian negative binomial model with parameter factorization, for which the optimal predictor can be derived by marginalization of likelihood over the posterior of the parameters.We first provide an efficient gibbs sampler for parameter inference in obsda.Then, we leverage the gene-gene network prior information and construct an informed and flexible variational family to infer the posterior distributions of model parameters.Comprehensive experiments on real-world rna-seq data demonstrate the superior performance of obsda, in terms of accuracy in identifying cancer subtypes by utilizing data from different domains.Moreover, we show that by taking advantage of the prior network information we can further improve the performance.Availability and implementation the source code for implementations of obsda and si-obsda are available at the following link.Supplementary information supplementary data are available at bioinformatics online.

Journal: Bioinformatics (Oxford, England) (2021)
Publication types: Journal Article
Development of a Web-based Curriculum to Prepare Diagnostic Radiology Residents during Post-Graduate Year 1 by Promoting Learning via Spaced Repetition and Interim Testing: If You Build It, Will They Come?

Rationale and objectives the purpose of this pilot project was to determine the feasibility of creating a single web-based resource to allow independent study for pre-radiology interns during their first post-graduate year of training, and to measure intern use of and satisfaction with this resource.Materials and methods a web-based curriculum, based on the principles of spaced learning and interim testing, was created and housed on an institutional learning management system.The curriculum consisted of narrated, interactive learning modules, electronic flashcards, and quizzes.We monitored the use of this curriculum by six pre-radiology interns.Surveys were completed to assess resident satisfaction.Results 73% of the total learning modules were completed.Of the completed modules, 90% were completed in either the first or the last three months of the study.The total hours spent reviewing the flashcards during the entire study period ranged from <1 to 7 hours.67% of the quizzes were completed.Survey results showed that the learners perceived the course as a useful resource and reported high satisfaction with the curriculum.Conclusion creating a web-based curriculum capable of monitoring intern use is feasible.There was variable use of the different components of the curriculum with clear clustering of use at the beginning and end of the study period.The users perceived the course as a useful resource and reported high satisfaction with the curriculum.

Journal: Academic radiology (2019)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Near-Infrared Light-Driven Photoredox Catalysis by Transition-Metal-Complex Nanodots.

Developing light-harvesting materials with broad spectral response is of fundamental importance in full-spectrum solar energy conversion.We found that, when a series of earth-abundant metal (cu, co, ni and fe) salts are dissolved in coordinating solvents uniformly dispersed nanodots (nds) are formed rather than fully dissolving as molecular species.The previously unrecognized formation of this condensed state is ascribed to spontaneous aggregation of molecular transition-metal-complexes (tmcs) via weak intermolecular interactions, which results in redshifted and broadened absorption into the nir region (200-1100 nm).Typical photoredox reactions, such as carbonylation and oxidative dehydrogenation, well demonstrate the feasibility of efficient utilization of nir light (λ>780 nm) by tmcs nds.Our finding provides a conceptually new strategy for extending the absorption towards low energy photons in solar energy harvesting and conversion via photoredox transformations.

Journal: Angewandte Chemie (International ed. in English) (2022)
Publication types: Journal Article
Impact of the Severity of Acquired von Willebrand Syndrome on the Short-Term Prognosis in Patients with Temporary Mechanical Circulatory Support.

And objectives:acquired von willebrand syndrome (avws) develops not only in patients with durable ventricular assist devices but also in patients receiving temporary mechanical circulatory support (mcs).However, its prognostic implication remains unknown.materials and methods:patients who received temporary mcs in our institute between august 2018 and september 2021 were included in this prospective study and the von willebrand factor multimer analyses were performed following the initiation of temporary mcs supports.The von willebrand factor large-multimer index was calculated as a normalized ratio of large-multimer proportion among total von willebrand factor.Association between the large-multimer index and the 30-day survival was investigated.results:a total of 31 patients (69 years old, 52% men) were included.Median large-multimer index was 63.0% (56.9%, 75.6%).The index was lowest in patients with extracorporeal membrane oxygenation than those receiving support from other devices.A lower index (<59.9%) was associated with lower 30-day survival (41.7% versus 94.7%,p= 0.001) with an odds ratio 0.044 (95% confidence interval 0.002-0.805,p= 0.035) adjusted for other potential confounders.conclusions:an advanced avws was associated with lower short-term survival in patients with temporary mcs.The clinical implication of avws-guided temporary mcs management remains the next concern.

Journal: Medicina (Kaunas, Lithuania) (2022)
Publication types: Journal Article
Six decades of change in pollution and benthic invertebrate biodiversity in a southern New England estuary.

Pollution has led to a decline of benthic invertebrate biodiversity of narragansett bay, raising questions about effects on ecosystem functions and services including shellfish production, energy flow to fishes, and biogeochemical cycles.Changes in community composition and taxonomic distinctness (biodiversity) were calculated from the 1950s-when quantitative benthic invertebrate data first became available-to 2015.Change in community composition of the bay was correlated with changes in dissolved inorganic nitrogen, dissolved oxygen, and sediment contaminants.A mid-bay reference site showed moderate changes in community composition but no change in biodiversity.In contrast, a more impacted site in the upper bay showed substantial differences in community composition over time and a decline in taxonomic distinctness.Bay-wide, as inputs of some stressors such as nutrients and sediment contaminants have declined, there are signs of recovery of benthic biodiversity but other stressors such as temperature and watershed development are increasing.

Journal: Marine pollution bulletin (2018)
Publication types: Journal Article
Triple-Wavelength Lasing with a Stabilized β-LaBSiO5:Nd3+Crystal.

Multi-wavelength lasers, especially the triple-wavelength laser around 1060 nm, could be produced by the4f3/2→4i11/2transition of nd3+and present numerous challenges and opportunities in the field of optoelectronics.The nd3+-doped high-temperature phase of la bsi o5(β-lbso) is an ideal crystal to produce triple-wavelength lasers; however, the crystal growth is challenging because of the phase transition from β-lbso to low-temperature phase (α-lbso) at 162 °c.This phase transition is successfully suppressed when the doping content of nd3+is larger than 6.3 at.%, and the nd3+-doped β-lbso is stable at room temperature.The local disorder of bo4tetrahedra due to nd3+doping is essential to the stabilization of β-lbso.For the first time, the β-lbso:8%nd3+crystal with a dimension of 1.8 × 1.8 × 1.8 cm3is obtained through the top-seeded solution method.The crystal shows strong optical absorption in the range of 785-815 nm, matching well with the commercial laser diode pumping source.The optical emission of4f3/2→4i11/2splits into four peaks with the highest optical emission cross section of 2.14 × 10-20cm2at 1068 nm.The continuous-wave triple-wavelength generation of coherent light at 1047, 1071, and 1092 nm is achieved with the highest output power of 235 m w and efficiency of 12.1%.

Journal: Journal of the American Chemical Society (2022)
Publication types: Journal Article
Blue-green roofs with forecast-based operation to reduce the impact of weather extremes.

Conventional green roofs have often been criticised for their limited water buffer capacity during extreme rainfall events and for their susceptibility to droughts when additional irrigation is unavailable.One solution to these challenges is to create an extra blue water retention layer underneath the green layer.Blue-green roofs allow more stormwater to be stored, and the reservoir can act as a water source for the green layer throughout capillary rises.An automated valve regulates the water level of the system.It can be opened to drain water when extreme precipitation is expected.Therefore, the water buffer capacity of the system during extreme rainfall events can be maximised by integrating precipitation forecasts as triggers for the operation of the valve.However, the added value of this forecast-based operation is yet unknown.Accordingly, in this study, we design and evaluate a hydrological blue-green roof model that utilises precipitation forecasts.We test its performance to capture (extreme) precipitation and to increase evapotranspiration and evaporative cooling under a variety of precipitation forecast-based decision rules.We show that blue-green roofs can capture between 70 % and 97 % of extreme precipitation (>20 mm/h) when set to anticipate ensemble precipitation forecasts from the european centre for medium-range weather forecasts (ecmwf).This capture ratio is considerably higher than that of a conventional green roof without extra water retention (12 %) or that of a blue-green roof that does not use forecast information (i.e., valve always closed; 59 %).Moreover, blue-green roofs allow for high evapotranspiration rates relative to potential evapotranspiration on hot summer days (around 70 %), which is higher than from conventional green roofs (30 %).This serves to underscore the higher capacity of blue-green roofs to reduce heat stress.Using the city of amsterdam as a case study, we show the high upscaling potential of the concept: on average, potentially suitable flat roofs cover 13.3 % of the total area of the catchments that are susceptible to pluvial flood risk.If the 90th percentile of the ecmwf forecast is used, an 84 % rainfall capture ratio can translate into capturing 11 % of rainfall in flood-prone urban catchments in amsterdam.

Journal: Journal of environmental management (2022)
Publication types: Journal Article
Nanoscale Infrared Spectroscopy Identifies Parallel to Antiparallel β-Sheet Transformation of Aβ Fibrils.

Spontaneous aggregation of amyloid beta (aβ) proteins leading to the formation of oligomers and eventually into fibrils has been identified as a key pathological signature of alzheimer's disease.The structure of late-stage aggregates have been studied in depth by conventional structural biology techniques, including nuclear magnetic resonance, x-ray crystallography, and infrared spectroscopy; however, the structure of early-stage aggregates is less known due to their transient nature.As a result, the structural evolution of amyloid aggregates from early oligomers to mature fibrils is still not fully understood.Here, we have applied atomic force microscopy-infrared nanospectroscopy to investigate the aggregation of aβ 16-22, which spans the amyloidogenic core of the aβ peptide.Our results demonstrate that aβ 16-22 involves a structural transition from oligomers with parallel β-sheets to antiparallel fibrils through disordered and possibly helical intermediate fibril structures, contrary to the known aggregation pathway of full-length aβ.

Journal: The journal of physical chemistry letters (2022)
Publication types: Journal Article
Blockade of ERK1/2 by U0126 alleviates uric acid-induced EMT and tubular cell injury in rats with hyperuricemic nephropathy.

Extracellular signal-regulated kinases 1 and 2 (erk1/2) are serine/threonine kinases and function as regulators of cellular proliferation and differentiation.Recently, we demonstrated that inhibition of erk1/2 alleviates the development and progression of hyperuricemia nephropathy (hn).However, its potential roles in uric acid-induced tubular epithelial-mesenchymal transition (emt) and tubular epithelial cell injury are unknown.In this study, we showed that hyperuricemic injury induced emt as characterized by downregulation of e-cadherin and upregulation of vimentin and snail1 in a rat model of hn.This was coincident with epithelial cells arrested at the g2/m phase of cell cycle, activation of notch1/jagged-1 and wnt/β-catenin signaling pathways, and upregulation of matrix metalloproteinase-2 (mmp-2) and mmp-9.Administration of u0126, a selective inhibitor of erk1/2, blocked all these responses.U0126 was also effective in inhibiting renal tubular cell injury, as shown by decreased expression of lipocalin-2 and kidney injury molecule-1 and active forms of caspase-3.U0126 or erk1/2 si rna can inhibit tubular cell emt and cell apoptosis as characterized with decreased expression of cleaved caspase-3.Moreover, erk1/2 inhibition suppressed hyperuricemic injury-induced oxidative stress as indicated by decreased malondialdehyde and increased superoxide dismutase.Collectively, erk1/2 inhibition-elicited renal protection is associated with inhibition of emt through inactivation of multiple signaling pathways and matrix metalloproteinases, as well as attenuation of renal tubule injury by enhancing cellular resistance to oxidative stress.

Journal: American journal of physiology. Renal physiology (2019)
Publication types: Journal Article;Research Support, N.I.H., Extramural;Research Support, Non-U.S. Gov't
Glycinergic Modulation of Pain in Behavioral Animal Models.

Animal models of human pain conditions allow for detailed interrogation of known and hypothesized mechanisms of pain physiology in awake, behaving organisms.The importance of the glycinergic system for pain modulation is well known; however, manipulation of this system to treat and alleviate pain has not yet reached the sophistication required for the clinic.Here, we review the current literature on what animal behavioral studies have allowed us to elucidate about glycinergic pain modulation, and the progress toward clinical treatments so far.First, we outline the animal pain models that have been used, such as nerve injury models for neuropathic pain, chemogenic pain models for acute and inflammatory pain, and other models that mimic painful human pathologies such as diabetic neuropathy.We then discuss the genetic approaches to animal models that have identified the crucial glycinergic machinery involved in neuropathic and inflammatory pain.Specifically, two glycine receptor (gly r) subtypes, gly rα1(β) and gly rα3(β), and the two glycine transporters (gly t), gly t1 and gly t2.Finally, we review the different pharmacological approaches to manipulating the glycinergic system for pain management in animal models, such as partialvs.Full agonism, reversibility, and multi-target approaches.We discuss the benefits and pitfalls of using animal models in drug development broadly, as well as the progress of glycinergic treatments from preclinical to clinical trials.

Journal: Frontiers in pharmacology (2022)
Publication types: Journal Article;Review
An Efficient Compression Method of Underwater Acoustic Sensor Signals for Underwater Surveillance.

In this paper, we propose a new compression method using underwater acoustic sensor signals for underwater surveillance.Generally, sonar applications that are used for surveillance or ocean monitoring are composed of many underwater acoustic sensors to detect significant sources of sound.It is necessary to apply compression methods to the acquired sensor signals due to data processing and storage resource limitations.In addition, depending on the purposes of the operation and the characteristics of the operating environment, it may also be necessary to apply compression methods of low complexity.Accordingly, in this research, a low-complexity and nearly lossless compression method for underwater acoustic sensor signals is proposed.In the design of the proposed method, we adopt the concepts of quadrature mirror filter (qmf)-based sub-band splitting and linear predictive coding, and we attempt to analyze an entropy coding technique suitable for underwater sensor signals.The experiments show that the proposed method achieves better performance in terms of compression ratio and processing time than popular or standardized lossless compression techniques.It is also shown that the compression ratio of the proposed method is almost the same as that of shorten with a 10-bit maximum mode, and both methods achieve a similar peak signal-to-noise ratio (psnr) and structural similarity (ssim) index on average.

Journal: Sensors (Basel, Switzerland) (2022)
Publication types: Journal Article
Evidence for amylose inclusion complexes with multiple acyl chain lipids using solid-state NMR and theoretical approaches.

Amylose is known to form inclusion complexes in the presence of hydrophobic guests.Among lipids, only single-chain fatty acids have been reported as possible guests with the surrounding amylose in a well-defined v-helix conformation.Using experimental13c solid-state nmr, we studied the formation of inclusion complexes between amylose and a variety of multiple-chains lipids of increasing complexity.Molecular dynamics simulations and calculations of13c isotropic chemical shifts using the density functional theory approach were performed to support the interpretation of experimental spectra.We provide unambiguous evidences that amylose forms inclusion complexes with lipids bearing multiple acyl chains.Amylose conformations around these lipids are characterized by {φ,ψ} anomeric bond dihedral angles near {115°,105°}.In the13c nmr spectra, this translates into c1and c4chemical shifts of 102.5 ppm and 81.1 ppm, regardless of the helical conformation of the amylose surrounding the acyl chains.

Journal: Carbohydrate polymers (2022)
Publication types: Journal Article
Effect of the Gant-Miwa-Thiersch Procedure for Rectal Prolapse on the Mesorectum.

Rectal prolapse (rp) most commonly occurs among elderly women and is caused by vulnerable suspensory tissue in the pelvis.In japan, the gant-miwa-thiersch procedure (gmt) is recommended for elderly people with poor general health.We retrospectively analyzed clinical data from 12 patients who underwent gmt at our hospital from september 2005 to july 2021 and investigated the effect of gmt on the mesorectum using abdominal-pelvic computed tomography (ct) performed for other diseases.The median age of the cohort was 82 years, and 92% of the subjects were women.The median rp length was 5 cm, and the median follow-up period was 60 months.Recurrence was observed in 1 of 12 patients (8.0%).Ct conducted before and more than 6 months after gmt revealed no abnormal findings in the mesorectum, whereas ct within 5 months after gmt revealed hyperdense fat in the mesorectum in all three patients (100%;p< 0.05).The rp recurrence rate after the gmt was low.The mechanism of the effect of gmt may involve not only a direct mucosal plicating effect but also adhesional rectosacral fixation due to the presence of inflammation extending to the mesorectum.

Journal: Journal of the anus, rectum and colon (2022)
Publication types: Case Reports;Journal Article
Investigation of Physicochemical and Sensory Quality Differences in Pork Belly and Shoulder Butt Cuts with Different Quality Grades.

The objective of this study was to investigate the effects of quality grade (qg) on the physicochemical composition and eating quality attributes of pork belly and shoulder butt.Seventy-two growing-finishing crossbred pigs were slaughtered and their carcasses were graded according to the korean pork carcass grading system.Based on the grading criteria, the carcasses were classified into: qg 1+(n=23), qg 1 (n=23) and qg 2 (n=26) groups.At 24 h postmortem, belly and shoulder butt cuts were collected from the qg groups and used for analysis of meat quality, flavor compounds and eating quality attributes.Results showed that the variation in fat content among qg was approximately 2% in the both cut types.The qg showed no effects on all the quality traits: cooking loss, p h and color of the belly or shoulder butt (p>0.05).Thirty-five flavor compounds comprising mainly fatty acids oxidation/degradation-derived products (e.g., aldehydes) and only few maillard reaction-derived products (e.g., sulfur-and nitrogen-containing compounds) were identified.However, the qg showed a minor effect on the flavor profiles in both the belly and shoulder butt.Regarding the sensory quality, no effects of the qg were found on all the eating quality attributes (color, flavor, juiciness, tenderness and acceptability) for both the belly and shoulder butt cuts (p>0.05).Thus, it may be concluded that the current pork carcass grading standards do not reflect the real quality and value of the belly and shoulder butt cuts.

Journal: Food science of animal resources (2021)
Publication types: Journal Article
Different Influences oftransFatty Acids on the Phospholipase A2 and Arachidonic Acid Metabolic Pathway in Hepatocytes.

This study investigated the effects of 9t18:1 (representing i-tfas), 9t16:1, and 11t18:1 (representing r-tfas) and their mixtures on the normal human hepatocyte lo2 cell function, the possible mechanism of lipid metabolism by lipidomics, and the relationship between phospholipase a2 (pla2) and the arachidonic acid (aa) metabolic pathway.Here, we found that the damaging effect of 9t18:1 on the lo2 cell function was significantly greater than those of 11t18:1 and 9t16:1 (p< 0.05), and the damaging effects of chb and hso were significantly greater than those of hhb and cm (p< 0.05).The lipidomic results showed that tfas and tfa mixtures caused a significant change in the lipid profiles of lo2 cells, in which the tag, pl, and ol contents increased significantly.Moreover, 9t18:1 regulated only the protein expression of c pla2 but did not participate in the aa metabolic pathway, while 11t18:1 and 9t16:1 participated in the cox-2 and cyp450 pathways, respectively.

Journal: Journal of agricultural and food chemistry (2021)
Publication types: Journal Article