syedzayyan/paper_mill_benchmark huggingface dataset:
Transcriptomic profiling of single circulating tumor cells provides insight into human metastatic gastric cancer.

Transcriptome analysis of circulating tumor cells (ctcs), which migrate into blood vessels from primary tumor tissues, at the single-cell level offers critical insights into the biology of metastasis and contributes to drug discovery.However, transcriptome analysis of single ctcs has only been reported for a limited number of cancer types, such as multiple myeloma, breast, hepatocellular, and prostate cancer.Herein, we report the transcriptome analysis of gastric cancer single-ctcs.We utilized an antigen-independent strategy for ctc isolation from metastatic gastric cancer patients involving a size-dependent recovery of ctcs and a single cell isolation technique.The transcriptomic profile of single-ctcs revealed that a majority of gastric ctcs had undergone epithelial-mesenchymal transition (emt), and indicated the contribution of platelet adhesion toward emt progression and acquisition of chemoresistance.Taken together, this study serves to employ ctc characterization to elucidate the mechanisms of chemoresistance and metastasis in gastric cancer.

Journal: Communications biology (2022)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Patient-specific three-dimensional printing spine model for surgical planning in AO spine type-C fracture posterior long-segment fixation.

The aim of this study was to compare duration of surgery, intraoperative fluoroscopy exposure, blood loss and the accuracy of pedicular screw placement between 3d model-assisted surgery and conventional surgery for ao spinal c-type injuries.Methods in this study 32 patients who were admitted with thoracolumbar ao spinal c-type injuries were included.These patients were divided randomly into two groups of 16 where one group was operated on using conventional surgery and the other group was operated on using 3d model-assisted surgery.During surgery, instrumentation time, amount of blood loss and intraoperative fluoroscopy exposure were recorded.Moreover, the status of the screws in the pedicles was assessed as described by learch and wiesner's and regional sagittal angles (rsa) were measured preop and postoperatively.Results it was found that there was a statistically significant difference in instrumentation time, blood loss and intraoperative fluoroscopy exposure in the 3d model-assisted surgery group (61.9 ± 4.7 min, 268.4 ± 42.7 ml, 16.3 ± 1.9 times) compared to the conventional surgery group (75.5 ± 11.0 min, 347.8 ± 52.2 m l, 19.7 ± 2.4 times) (t=4.5325, p < 0.0001 and t=4.7109, p < 0.0001 and t=4.4937, p < 0.0001, respectively) although the screw misplacement rate of the conventional surgery group was higher than that of the 3d model-assisted surgery group, the only statistically significant difference was in the medial axial encroachment (t=5.101 p=0.02) .There was no severe misplacement of pedicle screws in either group.There were no statistically significant differences between postoperative rsa angles and were in both groups restored significantly.Conclusion the results of this study have shown us that the 3d model helps surgeons see patients' pathoanatomy and determine rod lengths, pedicle screw angles and lengths preoperatively and peroparatively, which in turn shortens operative time, reduces blood loss and fluoroscopy exposure.Level of evidence level i, therapeutic study.

Journal: Acta orthopaedica et traumatologica turcica (2022)
Publication types: Journal Article;Randomized Controlled Trial
Storage media and RNA extraction approaches substantially influence the recovery and integrity of livestock fecal microbial RNA.

There is growing interest in understanding gut microbiome dynamics, to increase the sustainability of livestock production systems and to better understand the dynamics that regulate antibiotic resistance genes (i.e., the resistome).High-throughput sequencing of rna transcripts (rna-seq) from microbial communities (metatranscriptome) allows an unprecedented opportunity to analyze the functional and taxonomical dynamics of the expressed microbiome and emerges as a highly informative approach.However, the isolation and preservation of high-quality rna from livestock fecal samples remains highly challenging.This study aimed to determine the impact of the various sample storage and rna extraction strategies on the recovery and integrity of microbial rna extracted from selected livestock (chicken and pig) fecal samples.Methods fecal samples from pigs and chicken were collected from conventional slaughterhouses.Two different storage buffers were used at two different storage temperatures.The extraction of total rna was done using four different commercially available kits and rna integrity/quality and concentration were measured using a bioanalyzer 2100 system with rna 6000 nano kit (agilent, santa clara, ca, usa).In addition, rt-q pcr was used to assess bacterial rna quality and the level of host rna contamination.Results the quantity and quality of rna differed by sample type (i.e., either pig or chicken) and most significantly by the extraction kit, with differences in the extraction method resulting in the least variability in pig feces samples and the most variability in chicken feces.Considering a tradeoff between the rna yield and the rna integrity and at the same time minimizing the amount of host rna in the sample, a combination of storing the fecal samples in rnalater at either 4 °c (for 24 h) or -80 °c (up to 2 weeks) with extraction with pm kit (rneasy power microbiome kit) had the best performance for both chicken and pig samples.Conclusion our findings provided a further emphasis on using a consistent methodology for sample storage, duration as well as a compatible rna extraction approach.This is crucial as the impact of these technical steps can be potentially large compared with the real biological variability to be explained in microbiome and resistome studies.

Journal: PeerJ (2022)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Evaluation of work-related musculoskeletal problems in pediatric surgeons.

Pediatric surgeons are exposed to intense work-related activities, depending on their profession, including residency training.This study aims to investigate the musculoskeletal symptoms and analyze the relationship between musculoskeletal symptoms and the demographics, physical activity levels, and body mass index (bmi) of pediatric surgeons.Methods a total of 82 pediatric surgeons (female, 20; male, 62) were included in this study.The musculoskeletal symptoms were determined using the cornell musculoskeletal discomfort questionnaire.The levels of physical activity were determined using the international physical activity questionnaire.Results the mean age of the participants was 48.97 ± 8.894 years, the mean bmi was 26.72 ± 4.12 kg/m2, and the mean working time after acquiring their specialty was 18.65 ± 9.83 years.The average surgery counts per week were 15.22 ± 12.17.Pediatric surgeons mostly complained from lower back pain, upper back pain, neck pain, and right and left shoulder pain.Surgeons with higher bmi had higher pain scores and received more treatment sessions.Conclusions pediatric surgeons' complaints are related to their total numbers of surgery.Higher bmi and lower physical activity seem to be the major contributing factors for developing musculoskeletal symptoms.The study results indicated that surgeons should keep their bmi levels to the optimum and increase their physical activity levels.

Journal: Pediatric surgery international (2021)
Publication types: Journal Article
Bilateral Sacrospinous Hysteropexy Versus Bilateral Sacrospinous Ligament Fixation with Vaginal Hysterectomy for Apical Uterovaginal Prolapse.

The aim of this retrospective study was to compare the anatomical and functional outcomes between bilateral sacrospinous hysteropexy (bshp) and bilateral sacrospinous ligament fixation with vaginal hysterectomy (bslf/vh) in women with apical-predominant uterovaginal prolapse.Methods clinical data from patients with symptomatic pelvic organ prolapse-quantification (pop-q) stage 2 or higher uterovaginal prolapse who underwent either bshp (48 patients) or bslf/vh (69 patients) between january 2014 and december 2018 were reviewed retrospectively.The primary outcome was the subjective satisfaction rate evaluated by patient global impression of improvement, and the secondary outcomes included objective anatomical success rates, impact on disease-specific quality of life evaluated by the pelvic organ prolapse/urinary incontinence sexual questionnaire-12, pelvic floor distress inventory-short form 20, and pelvic floor impact questionnaire 7, and surgical complications.Results after a median follow-up of 35 months (range, 25-58 months), all patients in both groups demonstrated significant postoperative improvements in anatomical and functional outcomes (p<0.001).There were no significant differences in postoperative subjective and objective results, sexual satisfaction outcomes, or disease-specific quality of life between the bshp and bslf/vh groups, and similar incidence rates of intraoperative and postoperative complications were also recorded.Conclusion the uterus-sparing bshp procedure yielded noninferior anatomical and functional outcomes compared to the bslf/vh procedure and could be adopted as an alternative to conventional hysterectomy-based native-tissue repair modalities for symptomatic apical-predominant uterovaginal prolapse.

Journal: International neurourology journal (2022)
Publication types: Journal Article
Quantitative determination of albumin and immunoglobulin in human serum using gold nanoclusters.

In this experimental study, we developed a simple and selective approach to determine the concentrations of human serum albumin (hsa) and total amount of immunoglobulins (ig) in real human serum (hs) sample using luminescent gold nanoclusters (au ncs).In doing so, au ncs were grown directly on the hs proteins without any sample pretreatment.We synthesized au ncs on hsa and ig and studied their photophysical properties.Using combined fluorescent and colorimetric assay we were able to obtain protein concentrations with a high degree of accuracy relative to techniques currently used in clinical diagnostics.We used method of standard additions to determine both hsa and ig concentrations in hs by the au ncs absorbance and fluorescence signals.A simple and cost-effective method developed in this work represents an excellent alternative to the techniques currently used in clinical diagnostics.

Journal: Spectrochimica acta. Part A, Molecular and biomolecular spectroscopy (2023)
Publication types: Journal Article
Therapy-Resistant Ventricular Arrhythmias Developed More Often in Advanced Than in Therapeutic Mild Hypothermic Condition.

Therapy-resistant ventricular arrhythmias can occur during accidental advanced hypothermic conditions.On the other hand, hypothermic therapy using mild cooling has been successfully accomplished with infrequent ventricular arrhythmia events.to further clarify the therapeutic-resistant arrhythmogenic substrate which develops in hypothermic conditions, an experimental study was performed using a perfusion wedge preparation model of porcine ventricle, and electrophysiological characteristics, inducibility of ventricular arrhythmias, and effects of therapeutic interventions were assessed at 3 target temperatures (37, 32 and 28°c).as the myocardial temperature decreased, myocardial contractions and the number of spontaneous beats deceased.Depolarization (qrs width, stimulus-qrs interval) and repolarization (qt interval, erp) parameters progressively increased, and dispersion of the ventricular repolarization increased.At 28°c, vf tended to be inducible more frequently (1/11 at 37°c, 1/11 at 32°c, and 5/11 hearts at 28°c), and some vfs at 28°c required greater defibrillation energy to resume basic rhythm.an advanced but not a mild hypothermic condition had an enhanced arrhythmogenic potential in our model.In the advanced hypothermic condition, vf with relatively prolonged f-f intervals and a greater defibrillation energy were occasionally inducible based on the arrhythmogenic substrate characterized as slowed conduction and prolonged repolarization of the ventricle.

Journal: International heart journal (2019)
Publication types: Comparative Study;Journal Article
Extensive Genome-Wide Phylogenetic Discordance Is Due to Incomplete Lineage Sorting and Not Ongoing Introgression in a Rapidly Radiated Bryophyte Genus.

The relative importance of introgression for diversification has long been a highly disputed topic in speciation research and remains an open question despite the great attention it has received over the past decade.Gene flow leaves traces in the genome similar to those created by incomplete lineage sorting (ils), and identification and quantification of gene flow in the presence of ils is challenging and requires knowledge about the true phylogenetic relationship among the species.We use whole nuclear, plastid, and organellar genomes from 12 species in the rapidly radiated, ecologically diverse, actively hybridizing genus of peatmoss (sphagnum) to reconstruct the species phylogeny and quantify introgression using a suite of phylogenomic methods.We found extensive phylogenetic discordance among nuclear and organellar phylogenies, as well as across the nuclear genome and the nodes in the species tree, best explained by extensive ils following the rapid radiation of the genus rather than by postspeciation introgression.Our analyses support the idea of ancient introgression among the ancestral lineages followed by ils, whereas recent gene flow among the species is highly restricted despite widespread interspecific hybridization known in the group.Our results contribute to phylogenomic understanding of how speciation proceeds in rapidly radiated, actively hybridizing species groups, and demonstrate that employing a combination of diverse phylogenomic methods can facilitate untangling complex phylogenetic patterns created by ils and introgression.

Journal: Molecular biology and evolution (2021)
Publication types: Comparative Study;Journal Article;Research Support, Non-U.S. Gov't
Self-assembled nanomedicine combining a berberine derivative and doxorubicin for enhanced antitumor and antimetastatic efficacy via mitochondrial pathways.

Mitochondria play a central role in cancer progression and tumor metastasis, and nanomedicines targeting mitochondria have emerged as a promising strategy for tumor therapy.However, mitochondria targeting strategies have not been widely explored in the inhibition of tumor metastasis, and they have disadvantages of complicated preparation, low drug loading, systemic toxicity of the carriers and poor accumulation at tumor sites.Here we firstly developed self-assembled nanodrugs with a high drug loading (∼68%) comprised of a berberine derivative (ber) and doxorubicin (dox) by a simple nano-precipitation method, which successfully altered the target location of dox from the nucleus to mitochondria and therefore inhibited the proliferation, invasion and migration of mda-mb-231 cells by triggering cell apoptosis.The surface of nanodrugs was modified with dspe-peg-folic acid (dspe-peg-fa) and hyaluronic acid (ha) for precise tumor recognition and enhanced accumulation (ha-fa-bd nds).Upon arrival at the tumor site with the help of the enhanced permeability and retention (epr) effect, the partial degradation of ha by hyaluronidase (haase) at the tumor site allowed the partial exposure of the positively charged fa-bd nds to the cells, then nanodrugs would accumulate and enter tumor cells by dual binding to both folic acid (fa) and cd-44 receptors.Once internalized into lysosomes, both the ha outer shell and dspe-peg-fa of nanodrugs were degraded or decomposed completely to expose positively charged bd nds.Driven by delocalized lipophilic cations, nanodrugs could escape from lysosomes and reach mitochondria to induce a cascade reaction and finally cell apoptosis, as well as suppressing matrix metalloprotease (mmp)-2 and -9 activities and finally cell migration and invasion.In a xenograft mice model of mda-mb-231 breast cancer cells, the nanodrugs repaired the defects in mfn 1/drp 1 mitochondrial proteins, suppressed the activity of mmp-2 and -9, and significantly inhibited tumor cell proliferation and pulmonary metastasis.Our study showed a promising strategy for the treatment of metastatic breast cancer by targeting mitochondria followed by enhanced apoptosis.

Journal: Nanoscale (2021)
Publication types: Journal Article
From guidelines to practice: a pharmacist-driven prospective audit and feedback improvement model for peri-operative antibiotic prophylaxis in 34 South African hospitals.

Few data exist on the implementation of process measures to facilitate adherence to peri-operative antibiotic prophylaxis (pap) guidelines in africa.Objectives to implement an improvement model for pap utilizing existing resources, in order to achieve a reduction in surgical site infections (ssis) across a heterogeneous group of 34 urban and rural south african hospitals.Methods a pharmacist-driven, prospective audit and feedback strategy involving change management and improvement principles was utilized.This 2.5 year intervention involved a pre-implementation phase to test a pap guideline and a 'toolkit' at pilot sites.Following antimicrobial stewardship committee and clinician endorsement, the model was introduced in all institutions and a survey of baseline ssi and compliance rates with four process measures (antibiotic choice, dose, administration time and duration) was performed.The post-implementation phase involved audit, intervention and monthly feedback to facilitate improvements in compliance.Results for 70 weeks of standardized measurements and feedback, 24 206 surgical cases were reviewed.There was a significant improvement in compliance with all process measures (composite compliance) from 66.8% (95% ci 64.8-68.7) to 83.3% (95% ci 80.8-85.8), representing a 24.7% increase ( p < 0.0001).The ssi rate decreased by 19.7% from a mean group rate of 2.46 (95% ci 2.18-2.73) pre-intervention to 1.97 post-intervention (95% ci 1.79-2.15) ( p = 0.0029).Conclusions the implementation of process improvement initiatives and principles targeted to institutional needs utilizing pharmacists can effectively improve pap guideline compliance and sustainable patient outcomes.

Journal: The Journal of antimicrobial chemotherapy (2017)
Publication types: Journal Article
Untargeted Metabolomics Reveal Lipid Alterations upon 2-Deoxyglucose Treatment in Human HaCaT Keratinocytes.

The glucose analogue 2-deoxyglucose (2-dg) impedes cancer progression in animal models and is currently being assessed as an anticancer therapy, yet the mode of action of this drug of high clinical significance has not been fully delineated.In an attempt to better characterize its pharmacodynamics, an integrative uplc-q-exactive-based joint metabolomic and lipidomic approach was undertaken to evaluate the metabolic perturbations induced by this drug in human ha ca t keratinocyte cells.R-xcms data processing and subsequent multivariate pattern recognition, metabolites identification, and pathway analyses identified eight metabolites that were most significantly changed upon a 3 h 2-dg exposure.Most of these dysregulated features were emphasized in the course of lipidomic profiling and could be identified as ceramide and glucosylceramide derivatives, consistently with their involvement in cell death programming.Even though metabolomic analyses did not generally afford such clear-cut dysregulations, some alterations in phosphatidylcholine and phosphatidylethanolamine derivatives could be highlighted as well.Overall, these results support the adequacy of the proposed analytical workflow and might contribute to a better understanding of the mechanisms underlying the promising effects of 2-dg.

Journal: Journal of proteome research (2018)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Perceptions of Training Pathways from Recent Cardiothoracic Surgery Graduates.

There are three cardiothoracic surgery (cts) training pathways-general surgery residency followed by a cts residency of 2-3 years (traditional), 4 years of general surgery and 3 years of cts residency (4+3), and an integrated 6-year pathway (i-6).The goal of this study was to survey early career cardiothoracic surgeons regarding their training experiences.Methods an email-based survey was sent to cardiothoracic surgeons, who graduated between 2012-2017.Data on training pathway specific variables and overall satisfaction were collected.The primary endpoints were career preparation and satisfaction, scored on a scale from 1-100, 100 being the most positive.Results four hundred seventy-seven emails were sent, with a response rate of 95/477 (20%).Seventy-six of the respondents (80%) were male; the mean age was 39.Seventy-seven (81.0%) completed a traditional training pathway, 7 (7.4%) completed a 4+3 pathway, and 11 (11.6%) completed an i-6 pathway.Participants felt prepared for practice with a mean response of 79.8 (range 31-100); mean career satisfaction was 87.6.When asked which pathway respondents would choose in the current era, 52 (54.7%) would choose a traditional pathway, 17 (17.9%) a 4+3 pathway, and 19 (20.0%) an i-6 program; 7 (7.4%) did not respond.Twenty of 72 (27.8%) traditional pathway trained and 18/18(100%) integrated pathway trained surgeons would choose an integrated pathway.Conclusions this is the first survey addressing perceptions of training from early-career cardiothoracic surgeons across all training pathways.Data from this study provides insights to better understand how to improve cts training for the next generation of surgeons.

Journal: The heart surgery forum (2021)
Publication types: Journal Article
Topological phase transition and evolution of edge states in In-rich InGaN/GaN quantum wells under hydrostatic pressure.

Combining the k · p method with the third-order elasticity theory, we perform a theoretical study of the pressure-induced topological phase transition and the pressure evolution of topologically protected edge states in in n/ga n and in-rich in ga n/ga n quantum wells.We show that for a certain range of the quantum well parameters, thanks to a negative band gap pressure coefficient, it is possible to continuously drive the system from the normal insulator state through the topological insulator into the semimetal phase.The critical pressure for the topological phase transition depends not only on the quantum well thickness but also on the width of the hall bar, which determines the coupling between the edge states localized at the opposite edges.We also find that in narrow hall bar structures, near the topological phase transition, a significant rashba-type spin splitting of the lower and upper branches of the edge state dispersion curve appears.This effect originates from the lack of the mirror symmetry of the quantum well potential caused by the built-in electric field, and can be suppressed by increasing the hall bar width.When the pressure increases, the energy dispersion of the edge states becomes more parabolic-like and the spin splitting decreases.A further increase of pressure leads to the transition to a semimetal phase, which occurs due to the closure of the indirect 2d bulk band gap.The difference between the critical pressure at which the system becomes semimetallic, and the pressure for the topological phase transition, correlates with the variation of the pressure coefficient of the band gap in the normal insulator state.

Journal: Journal of physics. Condensed matter : an Institute of Physics journal (2017)
Publication types: Journal Article