syedzayyan/paper_mill_benchmark huggingface dataset:
A genome-wide association study of suicide attempts in the million veterans program identifies evidence of pan-ancestry and ancestry-specific risk loci.

To identify pan-ancestry and ancestry-specific loci associated with attempting suicide among veterans, we conducted a genome-wide association study (gwas) of suicide attempts within a large, multi-ancestry cohort of u.s.Veterans enrolled in the million veterans program (mvp).Cases were defined as veterans with a documented history of suicide attempts in the electronic health record (ehr; n = 14,089) and controls were defined as veterans with no documented history of suicidal thoughts or behaviors in the ehr (n = 395,064).Gwas was performed separately in each ancestry group, controlling for sex, age and genetic substructure.Pan-ancestry risk loci were identified through meta-analysis and included two genome-wide significant loci on chromosomes 20 (p = 3.64 × 10-9) and 1 (p = 3.69 × 10-8).A strong pan-ancestry signal at the dopamine receptor d2 locus (p = 1.77 × 10-7) was also identified and subsequently replicated in a large, independent international civilian cohort (p = 7.97 × 10-4).Additionally, ancestry-specific genome-wide significant loci were also detected in african-americans, european-americans, asian-americans, and hispanic-americans.Pathway analyses suggested over-representation of many biological pathways with high clinical significance, including oxytocin signaling, glutamatergic synapse, cortisol synthesis and secretion, dopaminergic synapse, and circadian rhythm.These findings confirm that the genetic architecture underlying suicide attempt risk is complex and includes both pan-ancestry and ancestry-specific risk loci.Moreover, pathway analyses suggested many commonly impacted biological pathways that could inform development of improved therapeutics for suicide prevention.

Journal: Molecular psychiatry (2022)
Publication types: Journal Article;Meta-Analysis;Research Support, Non-U.S. Gov't;Research Support, U.S. Gov't, Non-P.H.S.
Modelling hydrological strength and alteration in moribund deltaic India.

The ganga-brahmaputra moribund deltaic floodplain region hosted many socio-ecologically precious freshwater wetland ecosystems experiencing hydrological alteration.The present study aimed to model hydrological strength (hs) to show the spatial difference and account for the degree and direction of hydrological alteration of indian moribund deltaic wetland in three phases e.g.(1) phase i (1988-1997), (2) phase ii (1998-2007) and phase iii (2008-2017).Three key hydrological parameters, such as water presence frequency (wpf), water depth, and hydro-period were considered for hydrological strength modelling using two ensemble machine learning (ml) techniques (random forest (rf) and xgboost).Image algebra was employed for phasal change detection.Hydrological strength models show that around 75% of the wetland area was lost in-between phases i to iii and the loss was found more intensive in moderate and weak hs zones.Existing wetland shows a clear spatial difference of hs between wetland core and periphery and river linked and delinked or not linked wetlands.Regarding the suitability of the ml models, both are acceptable, however, the xgboost outperformed in reference to applied 15 statistical validation techniques and field evidence.Hs models based on change detection clarified that more than 22% and 55% of the weak hs zone in phases ii and iii respectively were turned into non-wetland.The degree of alteration revealed that about 40% of wetland areas experienced a negative alteration during phases i to ii, and this proportion increased to 63% in between phases ii to iii.Since the study figured out the spatial nature of hs, degree and direction of alteration at a spatial scale, these findings would be instrumental for adopting rational planning towards wetland conservation and restoration.

Journal: Journal of environmental management (2022)
Publication types: Journal Article
Hybrid Virtual Commissioning of a Robotic Manipulator with Machine Vision Using a Single Controller.

Digital twin (dt) is an emerging key technology that enables sophisticated interaction between physical objects and their virtual replicas, with applications in almost all engineering fields.Although it has recently gained significant attraction in both industry and academia, so far it has no unanimously adopted and established definition.One may therefore come across many definitions of what dt is and how to create it.Dt can be designed for an existing process and help us to improve it.Another possible approach is to create the dt for a brand new device.In this case, it can reveal how the system would behave in given conditions or when controlled.One of purposes of a dt is to support the commissioning of devices.So far, recognized and used techniques to make the commissioning more effective are virtual commissioning and hybrid commissioning.In this article, we present a concept of hybrid virtual commissioning.This concept aims to point out the possibility to use real devices already at the stage of virtual commissioning.It is introduced in a practical case study of a robotic manipulator with machine vision controlled with a programmable logic controller in a pick-and-place application.This study presents the benefits that stem from the proposed approach and also details when it is convenient to use it.

Journal: Sensors (Basel, Switzerland) (2022)
Publication types: Journal Article
Possibilities of valorization ofGnetumspp leaves in modern gastronomy: Production and characterization of new vegetable tarts and salads.

Gnetumspp is a green creeper plant abundantly found in the central african forests.Their leaves are eaten as vegetable by inhabitants.In order to valorize this vegetable in modern gastronomy, a survey was carried out in three towns of cameroon to evaluate its importance in the feeding habits.The leaves were also sliced in two different forms, precooked, spin-dried and used for gnetumtarts and salads production.50, 100 and 150 g of thin sliced precooked leaves were used to prepare three salads and three tarts, keeping the other ingredients constant.Three additional tarts were prepared similarly using thinnest sliced precooked leaves.The final products were analyzed in terms of physiochemical, nutritional and sensorial properties.More than 96.9% of people investigated eat gnetumleafy vegetables at least once per month.The survey study indicates that the transformation of gnetumis mostly done by people within the age of 20 to 40 years old.Results of the physicochemical analyses showed that the total protein, lipid and carbohydrate contents increased in general with the increasing of the gnetumleaf quantities used for preparation.The crude fiber contents of salads and tarts ranged from 52.00 ± 0.68 to 62.66 ± 1.26 and 29.33 ± 0.67 to 33.66 ± 0.47 g/100 g dw respectively.They were positively correlated with the quantity of gnetumleaves used.The total phenolic contents, also increased significantly (p < 0.05) with the quantity of gnetumleaves, from 182.45 ± 1.69 to 493.52 ± 2.10 mg/100 g dw for the salad and from 86.69 ± 4.08 to 283.21 ± 6.79 mg/100 g dw for the tart.The calculated energy density of tarts and salads permitted to classify these food products as low and high energy density foods respectively.The nutritional densities of produced tarts oscillated from 0.27 to 0.3 and that of salads from 0.58 to 0.71.With their nutritional values and the significant amount of fibers,gnetumtarts and salads could be good new recipes to valorize the gnetumleafy vegetables.

Journal: Heliyon (2023)
Publication types: Journal Article
Pediatric COVID-19 infection in Sulaimaniyah Governorate, Iraq.

Covid-19 is a severe acute respiratory syndrome caused by sars-co v-2.Objective to study the demographic and clinical presentations of covid-19 with their types including mis-c and kawasaki among children who were admitted to doctor jamal ahmad rashid pediatric teaching hospital (djarpth) at sulaimaniyah city, iraq.Patients and methods a prospective cohort study was conducted from june to december 2020 in which 50 cases suspected of covid-19 were enrolled in the study that was admitted at the first visit to the emergency department of djarpth and their age ranged between 3 months to 14 years.Then, the collected data were divided into 3 groups: covid-19, kawasaki disease (kd), and mis-c.Results the fever was the most common presented symptom in all cases with covid-19 regardless of the severity.Covid-19 may be presented as kd as well as mis-c.There is an increase in the number of kawasaki cases since 2019 by 6.7 fold due to the increased number of covid-19 cases in children.Death was more related to mis-c and primary covid-19 diseases.Most covid-19 cases presented with pericardial effusion; although coronary involvement and lv dysfunction mostly seen with mis-c cases.Conclusion covid-19 is not uncommon in pediatric patients and it presents as either primary, mis-c, and kd.Most of the deaths and icu outcomes were related to mis-c presentations.

Journal: American journal of otolaryngology (2022)
Publication types: Journal Article
Preserving Nasal Tip Rotation and Projection in Open Septorhinoplasty.

Open septorhinoplasty is a common facial plastic surgery procedure that requires extensive planning and knowledge to achieve predictable outcomes.Many patients want to keep their nasal tip characteristics, and the surgeon's task is to reliably meet this expectation and provide stable long-term results.Techniques used to reconstruct nasal tip support include the tongue-in-groove, caudal septal extension graft, and caudal septal replacement graft procedures.methods:we assessed the 1-year reliability of tongue-in-groove, caudal septal extension graft, and caudal septal replacement graft procedures in maintaining nasal tip rotation and projection in open septorhinoplasty.We conducted a retrospective case series review of septorhinoplasty cases between 2015 and 2019 at the medical university of south carolina.Cases with intention to change nasal tip rotation or projection were excluded.Two blinded reviewers analyzed standardized preoperative and 1-year postoperative photographs.results:fifty-seven patients fit the inclusion criteria and were included in the analysis.Mean preoperative and postoperative nasal tip rotations and projection ratios were similar (p=0.62,p=0.22, respectively).Twenty-six patients underwent a tongue-in-groove procedure, 24 had a caudal septal extension graft, and 7 had a caudal septal replacement graft with preoperative nasal tip rotations of 98.93°, 99.35°, and 96.89°, respectively (p=0.73).At 1 year, patients who received a tongue-in-groove procedure had a significant increase in nasal tip rotation to 101.24° (p=0.013), while patients who received a caudal septal extension graft had a significant decrease in nasal tip rotation to 97.25° (p=0.009).Patients who received a caudal septal replacement graft had no significant change in nasal tip rotation (p=0.117).The preoperative and postoperative projection ratios were not significantly different among the 3 techniques.conclusion:tongue-in-groove, caudal septal extension graft, and caudal septal replacement graft are reliable techniques for maintaining nasal tip projection in open septorhinoplasty.In our experience, when attempting to maintain preoperative nasal tip rotation, the tongue-in-groove technique resulted in a significant increase in tip rotation of 2.31°, while the caudal septal extension graft resulted in a significant decrease of 2.1° at 1 year postoperatively.

Journal: Ochsner journal (2022)
Publication types: Journal Article
A qualitative transcriptional signature of recurrence risk for stages II-III gastric cancer patients after surgical resection.

And aim metastasis is the leading cause of recurrence in gastric cancer.However, the imaging techniques and pathological examinations for tumor metastasis have a high false-positive rate or a high false-negative rate, and many proposed that metastasis-related molecular biomarkers can hardly be validated in independent datasets.Methods we propose to use significantly stable gene pairs with reversal relative expression orderings (reos) between non-metastasis and metastasis gastric cancer samples as the metastasis-related gene pairs.Based on the reos of these gene pairs, we developed a qualitative transcriptional signature for predicting the recurrence risk of stages ii-iii gastric cancer patients after surgical resection.Results a reos-based signature, consisting of 19 gene pairs (19-gps), was selected from 77 stages ii-iii gastric cancer patients and validated in two independent datasets.Samples in the high-risk group had shorter disease-free survival time and overall survival time than those in the low-risk group.Differentially expressed genes (degs) between the high- and low-risk groups classified by 19-gps were highly reproducible comparing with those between lymph node metastasis and lymph node non-metastasis groups.Functional enrichment analysis showed that these degs were significantly enriched in metastasis-related pathways, such as pi3k-akt and rap1 signaling pathways.The multi-omics analyses suggested that the epigenetic and genomic features might cause transcriptional differences between two subgroups, which help to characterize the mechanism of gastric cancer metastasis.Conclusions the signature could robustly identify patients at high recurrence risk after resection surgery, and the multi-omics analyses might aid in revealing the metastasis-related characteristics of gastric cancer.

Journal: Journal of gastroenterology and hepatology (2021)
Publication types: Journal Article
Profiling Cognitive Deficits in Intra-Axial and Extra-Axial Tumors Using Addenbrooke's Cognitive Examination as a Screening Tool: An Indian Experience.

Tumors of the brain, whether intra- or extra-axial, results in cognitive deficits.The aim of the present study was to profile cognitive deficits using addenbrooke's cognitive examination-malayalam (ace-m) as a screen and to determine the sensitivity and specificity of the same.Methods seventy-four drug naïve patients diagnosed to have brain tumors were assessed for cognitive functioning using ace-m before surgery.Results patients with high-grade intra-axial tumors showed a significant association on the cognitive domains of registration (0.04), recall (0.01), and visuospatial functioning (0.02).Gender showed an association between registration (0.02) and verbal fluency (0.02) with females performing better while education was significantly associated with retrograde or remote memory (0.00) with college-educated sample performing better.Significance was assumed at p< 0.05.In extra-axial tumors, laterality had a single association with recall (0.02).Males showed a significant cognitive decline on the cognitive domains of attention (0.02), recall (0.05), naming (0.02), and language functions (0.01).College educated group performed better on registration (0.01), recall (0.09), naming (0.00), and visuospatial functioning (0.00).The area under the receiver operating characteristic curve was estimated as 0.75, which indicates fairly good discriminative ability with a cut off of 71/100; sensitivity at 77.3 and specificity fixed at 67.Conclusions ace-m is capable of bringing out cognitive deficits along with a number of cognitive domains in patients with intra- and extra-axial tumors in the capacity of a screen, with fairly good levels of sensitivity and specificity.

Journal: Asian journal of neurosurgery (2017)
Publication types: Journal Article
Preliminary Findings on Proline-Rich Protein 14 as a Diagnostic Biomarker for Parkinson's Disease.

The nuclear envelope component proline-rich protein 14 (prr14) is involved in the nuclear morphological alteration and activation of the m tor (mammalian target of rapamycin) signaling pathway, and has been repeatedly shown to be upregulated in patients with parkinson's disease (pd).The aim of this study was to explore whether prr14 can be used as a potential biomarker for the diagnosis of pd.We compared prr14 expression in pd patients and normal controls in gene expression omnibus (geo) data.Quantitative enzyme-linked immunosorbent assay (elisa) was used to detect prr14 expression in pd patients and age- and sex-matched controls.The relationship between serum prr14 and clinical phenotype was evaluated using correlation analysis and logistic regression.The expression of prr14 in whole blood, substantia nigra, and medial substantia nigra was significantly higher in pd patients than in the healthy control group.Compared to plasma, serum was more suitable for the detection of prr14.Furthermore, serum prr14 level in pd patients was significantly higher than that in age- and sex-matched controls.The area under the curve for serum prr14 level in the ability to identify pd versus age- and sex-matched controls was 0.786.In addition, serum prr14 level was found to correlate with constipation in pd patients.Our findings demonstrate for the first time that serum prr14 is a potential biomarker for pd.

Journal: Neuromolecular medicine (2021)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Associations of Physician Characteristics with Sex Difference in Ischemic Heart Disease Incidence among Patients Living with Type 2 Diabetes in Taiwan.

(1) background: certain non-biological factors are suspected to explain the reduced sex difference in cardiovascular risk after diabetes.This study aimed to assess whether physician characteristics may account for such reduced sex difference.(2) methods: totally 10,105 type 2 diabetes patients (including 4962 men and 5143 women) were selected from taiwan's national health insurance claim data.The three-year period following the first day of clinical visit for type 2 diabetes in 2000 was set as the baseline period.The follow-up was made from the first day after baseline period to date of ischemic heart disease (ihd) incidence or censoring.Cox regression model was used to estimate hazard ratios (hrs) of ihd in relation to physician's characteristics.(3) results: the incidence of ihd for men and women was estimated at 17.47 and 15.96 per 1000 person-years, respectively.After controlling for socio-demographic variables and co-morbidity, male patients experienced a significantly higher hr than females for ihd (1.16, 95% confidence interval (ci) 1.04 to 1.29).Further adjustment for treatment adherence/continuity and physician characteristics resulted in essentially the same results.(4) conclusions: our study provides little support for the notation that physician characteristics may contribute to the reduced sex difference in ihd incidence in patients with type 2 diabetes.

Journal: Healthcare (Basel, Switzerland) (2021)
Publication types: Journal Article
Case Report of a Pelvic Kidney with Ureteral Obstruction from Inguinal Hernia Entrapment and Concurrent Cryptorchid Testis.

This is a case report of a ureteral obstruction from inguinal hernia entrapment with an ipsilateral cryptorchid testis in a 45-year-old male with an ectopic pelvic kidney.Ureteral herniation is unusual and to our knowledge has not been described in the setting of a patient with an ectopic pelvic kidney and undescended testis.The patient initially presented at an outside hospital with mild right lower quadrant abdominal pain and scrotal fullness, and initial computed tomography (ct) imaging demonstrated a pelvic right kidney with an indirect right inguinal hernia containing an entrapped ureter resulting in severe hydronephrosis.The ct also revealed an undescended testis on the patient's right side.A nephrostomy tube was then placed in the right kidney under interventional radiological (ir) guidance and subsequent ct urography showed resolution of hydronephrosis.Surgical hernia repair was followed up on a later date.The discussion addresses the unique pathological features of this case while highlighting the relevant complications of a ureteral herniation.Topics pelvic kidney, renal ectopia, ureteral obstruction, cryptorchidism, undescended testis.

Journal: Journal of education & teaching in emergency medicine (2022)
Publication types: Journal Article
Code-switching using aided AAC: toward an integrated theoretical framework.

Multilingual individuals who use augmentative and alternative communication (aac) often shift between language environments and speakers of different languages; thus, code-switching (or alternating between languages or dialects within or across contexts) becomes necessary for effective communication.Recently, aac product developers have responded to this need by building multilingual aac systems; however, research in multilingualism and aac is lacking.In this paper, we discuss theoretical and practical implications for research related to code-switching using aided aac.We use available literature investigating the sociolinguistic, psycholinguistic, and usage-based aspects of code-switching in spoken or signed modalities as a starting point for considering code-switching using aided aac.We present examples illustrating the varied expression of codeswitching across aided aac modalities and discuss directions for future research.

Journal: Augmentative and alternative communication (Baltimore, Md. : 1985) (2022)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Complex regional pain syndrome of the knee after conventional radiofrequency ablation of the genicular nerves treated successfully with dorsal root ganglion stimulation: A case report.

Radiofrequency (rf) treatment of the genicular nerves offers pain relief in patients suffering from chronic knee pain including persistent post-surgical knee pain (ppsp).We present the first case report of the development of complex regional pain syndrome (crps) in a chronic knee pain patient after an rf ablation of the genicular nerves that was successfully treated with dorsal root ganglion (drg) stimulation.Case presentation the patient developed increased pain, sympathetic and dysmorphic changes of the index knee 10 weeks after rf treatment for ppsp.Diagnosis of crps type ii was made using positive clinical findings and the budapest diagnostic tool.Laboratory workup and pet-ct were negative.The patient was refractory to usual care and she was treated successfully with dorsal ganglion root stimulation.Conclusions complex regional pain syndrome is a possible complication of rf ablation of the genicular nerves in patients with chronic knee pain, and drg stimulation may be a treatment option.Physicians should be aware of this complication, especially when patients have a medical history of crps.

Journal: Pain practice : the official journal of World Institute of Pain (2022)
Publication types: Case Reports;Journal Article