syedzayyan/paper_mill_benchmark huggingface dataset:
Reconstructing the genetic history of Italians: new insights from a male (Y-chromosome) perspective.

Due to its central and strategic position in europe and in the mediterranean basin, the italian peninsula played a pivotal role in the first peopling of the european continent and has been a crossroad of peoples and cultures since then.Aim this study aims to gain more information on the genetic structure of modern italian populations and to shed light on the migration/expansion events that led to their formation.Subjects and methods high resolution y-chromosome variation analysis in 817 unrelated males from 10 informative areas of italy was performed.Haplogroup frequencies and microsatellite haplotypes were used, together with available data from the literature, to evaluate mediterranean and european inputs and date their arrivals.Results fifty-three distinct y-chromosome lineages were identified.Their distribution is in general agreement with geography, southern populations being more differentiated than northern ones.Conclusions a complex genetic structure reflecting the multifaceted peopling pattern of the peninsula emerged: southern populations show high similarity with those from the middle east and southern balkans, while those from northern italy are close to populations of north-western europe and the northern balkans.Interestingly, the population of volterra, an ancient town of etruscan origin in tuscany, displays a unique y-chromosomal genetic structure.

Journal: Annals of human biology (2018)
Publication types: Journal Article
Sepsis Due to Haemophilus influenzae and Masked Influenza A Infection.

Haemophilus influenzae (h.Influenzae)is a facultative anaerobe, pleomorphic gram-negative coccobacillus capable of causing various respiratory and blood stream infections.Introduction of childhood immunization against h.Influenzatype b has decreased its prevalence.Invasive infection with non-typeable h.Influenzaeis increasing specially in vulnerable population.We present a case of a 69-year-old female who developed septic shock due to h.Influenzaeinfection.She was also found to have influenza a infection in bronchoalveolar lavage (bal) sample although initial test with nasopharyngeal swab was negative.This case report highlights the fact that in patients with high clinical suspicion, negative nasopharyngeal swab with polymerase chain reaction may not rule out influenza infection and bal may be necessary to confirm the diagnosis and h.Influenzaecan be causing bacterial superinfection in such patients.She was appropriately treated with third-generation cephalosporin for h.Influenzaeand with oseltamivir for influenza a.Her condition improved significantly with the treatment.

Journal: Cureus (2022)
Publication types: Case Reports;Journal Article
Single-cell technologies: From research to application.

In recent years, more and more single-cell technologies have been developed.A vast amount of single-cell omics data has been generated by large projects, such as the human cell atlas, the mouse cell atlas, the mouse rna atlas, the mouse atac atlas, and the plant cell atlas.Based on these single-cell big data, thousands of bioinformatics algorithms for quality control, clustering, cell-type annotation, developmental inference, cell-cell transition, cell-cell interaction, and spatial analysis are developed.With powerful experimental single-cell technology and state-of-the-art big data analysis methods based on artificial intelligence, the molecular landscape at the single-cell level can be revealed.With spatial transcriptomics and single-cell multi-omics, even the spatial dynamic multi-level regulatory mechanisms can be deciphered.Such single-cell technologies have many successful applications in oncology, assisted reproduction, embryonic development, and plant breeding.We not only review the experimental and bioinformatics methods for single-cell research, but also discuss their applications in various fields and forecast the future directions for single-cell technologies.We believe that spatial transcriptomics and single-cell multi-omics will become the next booming business for mechanism research and commercial industry.

Journal: Innovation (Cambridge (Mass.)) (2022)
Publication types: Journal Article;Review
Mapping open knowledge institutions: an exploratory analysis of Australian universities.

While the movement for open research has gained momentum in recent years, there remain concerns about the broader commitment to openness in knowledge production and dissemination.Increasingly, universities are under pressure to transform themselves to engage with the wider community and to be more inclusive.open knowledge institutions(okis) provide a framework that encourages universities to act with the principles of openness at their centre; not only should universities embrace digital open access (oa), but also lead actions in cultivating diversity, equity, transparency and positive changes in society.This leads to questions of whether we can evaluate the progress of okis and what are potential indicators for okis.As an exploratory study, this article reports on the collection and analysis of a list of potential oki indicators.Data for these indicators are gathered for 43 australian universities.The indicators provide high-dimensional and complex signals about university performances.They show evidence of large disparities in characteristics such as indigenous employment and gender equity, and a preference for repository-mediated oa across australian universities.We demonstrate use of the oki evaluation framework to categorise these indicators into three platforms of diversity, communication and coordination.The analysis provides new insights into the australian open knowledge landscape and ways of mapping different paths of okis.

Journal: PeerJ (2021)
Publication types: Journal Article
Rapid and Mild Synthesis of Amino Acid N-Carboxy Anhydrides: Basic-to-Acidic Flash Switching in a Microflow Reactor.

Polymerization of n-carboxy anhydrides (ncas) is the primary process used to prepare polypeptides.The synthesis of various pure ncas is key to the efficient synthesis of polypeptides.The only practical method that can be used to synthesize ncas requires harsh acidic conditions that make acid-labile substrates unusable and results in an undesired ring opening of ncas.Basic-to-acidic flash switching and subsequent flash dilution technology in a microflow reactor was used to demonstrate the synthesis of ncas.It is both rapid (0.1 s) and mild (20 °c) and includes substrates containing acid-labile functional groups.The basic-to-acidic flash switching enabled both an acceleration of the desired nca formation and avoided the undesired ring opening of ncas.The flash dilution precluded the undesired decomposition of acid-labile functional groups.The developed process allowed the synthesis of various ncas which cannot be readily synthesized using conventional batch methods.

Journal: Angewandte Chemie (International ed. in English) (2018)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
UPLC/MS-based untargeted metabolomics reveals the changes in muscle metabolism of electron beam irradiated Solenocera melantho during refrigerated storage.

Shrimp meat is an extremely perishable product; however, refrigeration can slow down spoilage.In this study, we used electron beam irradiation (ebi) to pre-treat shrimp meat and analyzed the metabolites of the treated shrimp meat during refrigerated storage using metabonomic analysis methods.In total, 4865 metabolites were identified, of which, 103 differential metabolites had kegg (kyoto encyclopedia of genes and genomes) ids.Further, two potential biomarkers were obtained.Based on the results, l-lysine was downregulated, while 2'-deoxyguanosine 5'-monophosphate and dihydroxyacetone phosphate acyl ester were upregulated during the refrigerated storage.The metabolic activity began to weaken gradually after 9 days.However, the different metabolites related to ebi were not identified herein.Nonetheless, the study findings revealed the metabolic changes in solenocera melantho at the molecular level during refrigerated storage after ebi.

Journal: Food chemistry (2022)
Publication types: Journal Article
The prevalence of thyroid dysfunction and autoimmune thyroid disease in patients with rheumatoid arthritis.

Rheumatoid arthritis (ra) is one of the most common chronic non-organ-specific autoimmune diseases; meanwhile, autoimmune thyroid disease (aitd) is the most common organ-specific autoimmune disease that can lead to hypo or hyperthyroidism.Although the etiology of both diseases is complex with a combination of genetic and environmental factors, there are overlaps in genes contributing to the pathogenesis of both diseases.Numerous studies found a correlation between thyroid abnormality and ra in different populations, yet some didn't.This study is aimed to evaluate the prevalence of thyroid dysfunction, aitd, and anti-thyroid peroxidase (anti-tpo) positively in iranian patients with ra.Methods a total of 250 ra patients and 248 patients with non-inflammatory rheumatologic disease were included in this case-control study.All participants underwent complete clinical and laboratory assessments.Participants were also assessed for thyroid function testing, including anti-tpo antibodies.Results thyroid dysfunction was twice as common in ra patients as in controls (or = 2.16; p-value > 0.001).Overt hypothyroidism was the most common thyroid dysfunction among ra patients (58 out of 84).Anti-tpo positivity was also significantly more common in ra compared with controls (or = 2.65; p-value > 0.001).The proportion of controls and ra patients with aitd were 9 and 21.5%, respectively.Aitd was found 2.8 times more common in ra group than controls (or = 2.77; p-value > 0.001).Conclusion it was demonstrated that ra was an independent factor associated with thyroid dysfunction and aitd.

Journal: BMC rheumatology (2022)
Publication types: Journal Article
Alternation between toxic and proliferative effects of Roundup® on human thyroid cells at different concentrations.

Endocrine-disrupting and carcinogenic effects of glyphosate have long been suspected, but little is known about the effect of compounds used in real life at different concentrations, neither in normal nor in thyroid tumor cells.As cancer cells may have different sensitivities and the effect of the product containing glyphosate may be different from that produced by the active ingredient alone, including the acceptable occupational exposure level (aoel=160μg/l) and the acceptable daily intake (adi=830μg/l) determined by anvisa, we used two human thyroid-derived cell lines, nthy-ori 3-1 (from normal follicular cells) and tpc-1 (from papillary carcinoma), to test 15 different concentrations of roundup® original di.Trypan blue (tb), cck-8 and brd u assays were used to evaluate cytotoxicity, metabolic activity and proliferation with 24h and 48h exposures in technical and biological triplicates.Tb showed an important toxic effect, especially after 24h of exposure, in both cell lines.The aoel concentration caused the death of 43% and 50% of the nthy-ori and tpc-1 cells, respectively, in 24 h, while adi resulted in 35% and 58% of cell death.After 48h of exposure, aoel and adi caused a lower number of dead nthy-ori (33% and 18%) and tpc-1 (33% and 37%) cells, respectively, suggesting that the toxic effect of the product disappears and/or both strains have repair mechanisms that protect them from longer exposures.On the other hand, the cck-8 assay showed that small concentrations of roundup have a proliferative effect: 6.5μg/l increased the number of both nthy-ori and tpc-1 cells at 24h, and the brd u assay confirmed the stimulatory effect with a 321% increase in the absorbance of nthy-ori cells at 48h.The herbicide produced even more frequent increases in the brd u absorbance of tpc-1 cells, mainly at 24h.We conclude that thyroid cells exposed to roundup present a nonmonotonic dual dose-response curve.Low concentrations of the pesticide, considered acceptable, cause significant cell death but also have an important proliferative effect, especially on tpc-1 cells.This herbicide, widely used around the world, may play a role in the increased incidence rate of thyroid nodules and cancer that has been observed in recent decades.

Journal: Frontiers in endocrinology (2022)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
ZFPM2-AS1 transcriptionally mediated by STAT1 regulates thyroid cancer cell growth, migration and invasion via miR-515-5p/TUSC3.

Our purpose was to study the roles and molecular mechanisms of long non-coding rna (lnc rna) zfpm2 antisense rna 1 (zfpm2-as1) in thyroid cancer.methods:firstly, the expression of zfpm2-as1, mi r-515-5p and tusc3 was detected in thyroid cancer tissues and cells.Secondary, their biological functions (proliferation, apoptosis, migration and invasion) were analyzed by a serious of functional experiments including cell counting kit-8 (cck-8), clone formation, 5-ethynyl-2'-deoxyuridine (ed u), enzyme-linked immunosorbent assay (elisa), wound healing and transwell assays.Thirdly, the mechanisms of stat1/zfpm2-as1 and zfpm2-as1/mi r-515-5p/tusc were validated using chromatin immunoprecipitation (chip), pull-down and luciferase reporter assays.results:zfpm2-as1 and tusc were both highly expressed and mi r-515-5p was down-regulated in thyroid cancer tissues as well as cells.Their knockdown weakened thyroid cancer cell growth, migration, and invasion.Zfpm2-as1 was mainly distributed in the nucleus and cytoplasm of thyroid cancer cells.Mechanistically, up-regulation of zfpm2-as1 was induced by transcription factor stat1 in line with chip and luciferase reporter assays.Furthermore, as a sponge of mi r-515-5p, zfpm2-as1 decreased the ability of mi r-515-5p to inhibit tusc3 expression by pull-down, luciferase reporter and gain-and-loss assays, thereby promoting malignant progression of thyroid cancer.conclusion:zfpm2-as1 acted as an oncogene in thyroid cancer, which was transcriptionally mediated by stat1.Furthermore, zfpm2-as1 weakened the inhibitory effect of mi r-515-5p on tusc3.Thus, zfpm2-as1 could be an underlying biomarker for thyroid cancer.

Journal: Journal of Cancer (2021)
Publication types: Journal Article
Rational Constructed Ultra-Small Iron Oxide Nanoprobes Manifesting High Performance forT1-Weighted Magnetic Resonance Imaging of Glioblastoma.

Precise diagnosis and monitoring of cancer depend on the development of advanced technologies for in vivo imaging.Owing to the merits of outstanding spatial resolution and excellent soft-tissue contrast, the application of magnetic resonance imaging (mri) in biomedicine is of great importance.Herein, angiopep-2 (ang), which can simultaneously help to cross the blood-brain barrier and target the glioblastoma cells, was rationally combined with the 3.3 nm-sized ultra-small iron oxide (fe3o4) to construct high-performance mri nanoprobes (fe3o4-ang nps) for glioblastoma diagnosis.The in vitro experiments show that the resultant fe3o4-ang nps not only exhibit favorable relaxation properties and colloidal stability, but also have low toxicity and high specificity to glioblastoma cells, which provide critical prerequisites for the in vivo tumor imaging.Furthermore, in vivo imaging results show that the fe3o4-ang nps exhibit good targeting ability toward subcutaneous and orthotopic glioblastoma model, manifesting an obvious contrast enhancement effect on the t1-weighted mr image, which demonstrates promising potential in clinical application.

Journal: Nanomaterials (Basel, Switzerland) (2021)
Publication types: Journal Article
Reliability and clinical feasibility of measuring dual-task gait in the inpatient rehabilitation setting following traumatic brain injury.

To prepare patients with traumatic brain injury (tbi) for discharge from inpatient rehabilitation, physical therapists may incorporate dual-task gait activities.Reliability of common dual-task measures for people with tbi in inpatient rehabilitation is undetermined.Our purpose was to assess inter-rater and intra-rater reliability and clinical feasibility of dual-task measures [walking while talking test (wwtt), modified walking and remembering task (m wart), timed up and go-cognitive (tug-cog)] in inpatient rehabilitation for patients with tbi.methods: a total of 22 individuals with tbi completing the dual-task measures (wwtt, walking and remembering task (wart), and tug-cog) in inpatient rehabilitation were rated concurrently by two physical therapists in a single testing session.Sessions were video recorded and rated by the same raters viewing the video 7-10 days later.Raters completed a survey assessing feasibility of conducting the dual-task measures in patients with tbi in inpatient rehabilitation.Data were analyzed by calculating icc(2,1)for inter-rater reliability and icc(3,1)for intra-rater reliability.results: all dual-task measures (wwtt, m wart, tug-cog) had excellent inter-rater and intra-rater reliability.Raters considered dual-task measures feasible for patients with tbi during inpatient rehabilitation.conclusions: the wwtt, m wart, and tug-cog have excellent reliability and appear clinically feasible for incorporation into clinical practice in inpatient rehabilitation following tbi.

Journal: Physiotherapy theory and practice (2019)
Publication types: Journal Article
Multiple Profile Models Extract Features from Protein Sequence Data and Resolve Functional Diversity of Very Different Protein Families.

Functional classification of proteins from sequences alone has become a critical bottleneck in understanding the myriad of protein sequences that accumulate in our databases.The great diversity of homologous sequences hides, in many cases, a variety of functional activities that cannot be anticipated.Their identification appears critical for a fundamental understanding of the evolution of living organisms and for biotechnological applications.Profile view is a sequence-based computational method, designed to functionally classify sets of homologous sequences.It relies on two main ideas: the use of multiple profile models whose construction explores evolutionary information in available databases, and a novel definition of a representation space in which to analyze sequences with multiple profile models combined together.Profile view classifies protein families by enriching known functional groups with new sequences and discovering new groups and subgroups.We validate profile view on seven classes of widespread proteins involved in the interaction with nucleic acids, amino acids and small molecules, and in a large variety of functions and enzymatic reactions.Profile view agrees with the large set of functional data collected for these proteins from the literature regarding the organization into functional subgroups and residues that characterize the functions.In addition, profile view resolves undefined functional classifications and extracts the molecular determinants underlying protein functional diversity, showing its potential to select sequences towards accurate experimental design and discovery of novel biological functions.On protein families with complex domain architecture, profile view functional classification reconciles domain combinations, unlike phylogenetic reconstruction.Profile view proves to outperform the functional classification approach panther, the two k-mer-based methods cupp and e cami and a neural network approach based on restricted boltzmann machines.It overcomes time complexity limitations of the latter.

Journal: Molecular biology and evolution (2022)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Efficacy and safety of long-acting growth hormone in adult growth hormone deficiency: A systematic review and meta-analysis.

& aims no meta-analysis has analysed efficacy and safety of long-acting growth hormone (gh) therapy in adult gh deficiency.We undertook this meta-analysis to address this gap in knowledge methods: electronic databases were searched for rcts involving adult gh deficiency patients receiving weekly long-acting gh as compared to daily gh/placebo controls.Primary outcome was to evaluate changes in body-composition parameters.Secondary outcomes were to evaluate alterations in glycaemia and adverse-events.Results data from 5 studies involving 648 patients were analysed (4 studies having daily gh as active controls; 1 study having placebo as passive controls).Over 24-34 weeks clinical use, patients receiving long-acting gh had comparable change in lean mass [md-0.28 kg (95%ci: 0.94 - 0.38); p = 0.41; i2= 29% (low heterogeneity)] and fat mass [md-0.10 kg (95%ci: 1.97-1.78); p = 0.92; i2= 77%(considerable heterogeneity)] as compared to daily gh injections.Long-acting gh use was associated with significantly lower visceral adipose tissue [md-1.75 cm2(95%ci: 2.14 to -1.35); p < 0.01; i2= 0% (low heterogeneity)] and higher gynoid fat-mass [md 0.14 kg(95%ci:0.02-0.26); p = 0.03] compared to daily gh injections.Total adverse events [risk ratio (rr) 1.65 (95% ci: 0.83-3.29); p = 0.15; i2= 68%] and severe adverse events [rr 0.60 (95% ci: 0.30-1.19); p = 0.14; i2= 0%] were not significantly different in long-acting gh group compared to controls.Occurrence of headache, arthralgia, nasopharyngitis, new onset diabetes, anti-gh antibodies were comparable among groups.Long-acting gh users had significantly higher treatment adherence compared to controls [or 4.80 (95%ci:3.58-6.02); p < 0.01; i2= 0%].Conclusion long-acting gh has comparable beneficial impact on body composition parameters in adult gh deficiency, is well tolerated without any increased adverse events.

Journal: Diabetes & metabolic syndrome (2022)
Publication types: Journal Article;Meta-Analysis;Systematic Review
Transcriptome Analysis and Screening of Genes Associated with Flower Size in Tomato (Solanum lycopersicum).

Flower development is not only an important way for tomato reproduction but also an important guarantee for tomato fruit production.Although more and more attention has been paid to the study of flower development, there are few studies on the molecular mechanism and gene expression level of tomato flower development.In this study, rna-seq analysis was performed on two stages of tomato flower development using the illumina sequencing platform.A total of 8536 degs were obtained by sequencing, including 3873 upregulated degs and 4663 down-regulated degs.These differentially expressed genes are related to plant hormone signaling, starch and sucrose metabolism.The pathways such as pentose, glucuronate interconversion, and phenylpropanoid biosynthesis are closely related and mainly involved in plant cellular and metabolic processes.According to the enrichment analysis results of degs, active energy metabolism can be inferred during flower development, indicating that flower development requires a large amount of energy and material supply.In addition, some plant hormones, such as ga, may also have effects on flower development.Combined with previous studies, the expression levels of solyc02g087860and three ofb zipswere significantly increased in the full flowering stage compared with the flower bud stage, indicating that these genes may be closely related to flower development.These genes were previously reported in arabidopsis but not in tomatoes.Our next work will conduct a detailed functional analysis of the identified b zip family genes to characterize their association with tomato flower size.This study will provide new genetic resources for flower formation and provide a basis for tomato yield breeding.

Journal: International journal of molecular sciences (2022)
Publication types: Journal Article