syedzayyan/paper_mill_benchmark huggingface dataset:
Estrogen receptor-positive (ER+) breast cancer treatment: Are multi-target compounds the next promising approach?

Endocrine therapy is currently the main therapeutic approach for estrogen receptor-positive (er+) breast cancer, the most frequent subtype of breast cancer in women worldwide.For this subtype of tumors, the current clinical treatment includes aromatase inhibitors (ais) and anti-estrogenic compounds, such as tamoxifen and fulvestrant, being ais the first-line treatment option for post-menopausal women.Moreover, the recent guidelines also suggest the use of these compounds by pre-menopausal women after suppressing ovaries function.However, besides its therapeutic efficacy, the prolonged use of this type of therapies may lead to the development of several adverse effects, as well as, endocrine resistance, limiting the effectiveness of such treatments.In order to surpass this issues and clinical concerns, during the last years, several studies have been suggesting alternative therapeutic approaches, considering the function of aromatase, erα and erβ.Here, we review the structural and functional features of these three targets and their importance in er+breast cancer treatment, as well as, the current treatment strategies used in clinic, emphasizing the importance of the development of multi-target compounds able to simultaneously modulate these key targets, as a novel and promising therapeutic strategy for this type of cancer.

Journal: Biochemical pharmacology (2020)
Publication types: Journal Article;Research Support, Non-U.S. Gov't;Review
Digital health for climate change mitigation and response: a scoping review.

Climate change poses a major threat to the operation of global health systems, triggering large scale health events, and disrupting normal system operation.Digital health may have a role in the management of such challenges and in greenhouse gas emission reduction.This scoping review explores recent work on digital health responses and mitigation approaches to climate change.Materials and methods we searched medline up to february 11, 2022, using terms for digital health and climate change.Included articles were categorized into 3 application domains (mitigation, infectious disease, or environmental health risk management), and 6 technical tasks (data sensing, monitoring, electronic data capture, modeling, decision support, and communication).The review was prisma-sc r compliant.Results the 142 included publications reported a wide variety of research designs.Publication numbers have grown substantially in recent years, but few come from low- and middle-income countries.Digital health has the potential to reduce health system greenhouse gas emissions, for example by shifting to virtual services.It can assist in managing changing patterns of infectious diseases as well as environmental health events by timely detection, reducing exposure to risk factors, and facilitating the delivery of care to under-resourced areas.Discussion while digital health has real potential to help in managing climate change, research remains preliminary with little real-world evaluation.Conclusion significant acceleration in the quality and quantity of digital health climate change research is urgently needed, given the enormity of the global challenge.

Journal: Journal of the American Medical Informatics Association : JAMIA (2022)
Publication types: Journal Article;Research Support, Non-U.S. Gov't;Review
Myeloid antigen-presenting cell niches sustain antitumor T cells and license PD-1 blockade via CD28 costimulation.

The mechanisms regulating exhaustion of tumor-infiltrating lymphocytes (til) and responsiveness to pd-1 blockade remain partly unknown.In human ovarian cancer, we show that tumor-specific cd8+til accumulate in tumor islets, where they engage antigen and upregulate pd-1, which restrains their functions.Intraepithelial pd-1+cd8+til can be, however, polyfunctional.Pd-1+til indeed exhibit a continuum of exhaustion states, with variable levels of cd28 costimulation, which is provided by antigen-presenting cells (apc) in intraepithelial tumor myeloid niches.Cd28 costimulation is associated with improved effector fitness of exhausted cd8+til and is required for their activation upon pd-1 blockade, which also requires tumor myeloid apc.Exhausted til lacking proper cd28 costimulation in situ fail to respond to pd-1 blockade, and their response may be rescued by local ctla-4 blockade and tumor apc stimulation via cd40l.

Journal: Cancer cell (2021)
Publication types: Journal Article;Research Support, N.I.H., Extramural;Research Support, Non-U.S. Gov't
Therapeutic Bronchoscopy for Lung Nodules: Where Are We Now?

Lobar resection has been the established standard of care for peripheral early-stage non-small cell lung cancer (nsclc).Over the last few years, surgical lung sparing approach (sublobar resection [slr]) has been compared with lobar resection in t1n0 nsclc.Three nonsurgical options are available in those patients who have a prohibitive surgical risk, and those who refuse surgery: stereotactic body radiotherapy (sbrt), percutaneous ablation, and bronchoscopic ablation.Local ablation involves placement of a probe into a tumor, and subsequent application of either heat or cold energy, pulsing electrical fields, or placement of radioactive source under an image guidance to create a zone of cell death that encompasses the targeted lesion and an ablation margin.Despite being in their infancy, the bronchoscopic ablative techniques are undergoing rapid research, as they extrapolate a significant knowledge-base from the percutaneous techniques that have been in the radiologist's armamentarium since 2000.Here, we discuss selected endoscopic and percutaneous thermal and non-thermal therapies with the focus on their efficacy and safety.

Journal: Seminars in respiratory and critical care medicine (2022)
Publication types: Journal Article
Abundance, Diversity, and Function of Soil Microorganisms in Temperate Alley-Cropping Agroforestry Systems: A Review.

Modern temperate alley-cropping systems combine rows of trees with rows of crops (agroforestry), which allows for diverse interspecific interactions such as the complementary and competitive use of resources.The complementary use of resources between trees and crops is considered the main advantage of these multifunctional land use systems over cropland monocultures.Moreover, several studies demonstrated that agroforestry systems are environmentally more sustainable than cropland monocultures.Over two decades of research on soil microorganisms in temperate alley-cropping systems are characterized by a variety of different methodological approaches and study designs to investigate the impact of agroforestry on the soil microbiome.Here, we review the available literature on the abundance, diversity, and functionality of soil microorganisms in temperate alley-cropping systems.Further, we identify current knowledge gaps as well as important experimental factors to consider in future studies.Overall, we found that temperate alley-cropping systems increase soil microbial abundance, diversity, and functions as compared to cropland monocultures, which is expected to contribute to enhanced biological soil fertility in these systems.

Journal: Microorganisms (2022)
Publication types: Journal Article;Review
Reference values of nuchal fold thickness in an Iranian population sample.

Considering that ethnicity and gestational age (ga) could affect the value of nuchal fold thickness (nft) in mid-trimester, we aimed to determine the reference intervals of nft values for each gestational week from 16 to 24 weeks of pregnancy among a group of iranian pregnant women.Materials and methods in this cross-sectional study, medical files of pregnant women who underwent fetal anomaly scanning at 16-24 weeks of gestation were reviewed and the following data were extracted: ga, value of nft, value of nuchal translucency (nt) in their previous ultrasound study, if available, and head circumference (hc).The 5th, 25th, 50th, 75th, and 95thpercentiles of nft for each gestational week were determined.The association between nft and hc, ga, and nt were also determined.Results medical files of 882 pregnant women were studied.The expected 95thpercentile value of nft between 16thand 24thweeks of gestation ranged from 4 mm to 5.9 mm.The mean (standard deviation) of nft increased with ga from 2.67 (0.90) mm at 16thweeks to 4.69 (0.71) mm at 24thweeks.There was a significant positive association between nft and ga (β = 1.11,p< 0.001), hc (β = 0.21,p< 0.001), and nt (β = 0.351,p< 0.001).Conclusion the findings of this study revealed that before the 20thweek of gestation, the appropriate cutoff value of nft is 5 mm, and for 21stto 24thweeks, the proper cutoff is 6 mm.However, for providing more conclusive results, further studies with larger sample size and considering the impact of other influencing variables are recommended.

Journal: Journal of research in medical sciences : the official journal of Isfahan University of Medical Sciences (2018)
Publication types: Journal Article
Lysosomal enzyme trafficking factor LYSET enables nutritional usage of extracellular proteins.

Mammalian cells can generate amino acids through macropinocytosis and lysosomal breakdown of extracellular proteins, which is exploited by cancer cells to grow in nutrient-poor tumors.Through genetic screens in defined nutrient conditions, we characterized lyset, a transmembrane protein (tmem251) selectively required when cells consume extracellular proteins.Lyset was found to associate in the golgi with glc nac-1-phosphotransferase, which targets catabolic enzymes to lysosomes through mannose-6-phosphate modification.Without lyset, glc nac-1-phosphotransferase was unstable because of a hydrophilic transmembrane domain.Consequently, lyset-deficient cells were depleted of lysosomal enzymes and impaired in turnover of macropinocytic and autophagic cargoes.Thus, lyset represents a core component of the lysosomal enzyme trafficking pathway, underlies the pathomechanism for hereditary lysosomal storage disorders, and may represent a target to suppress metabolic adaptations in cancer.

Journal: Science (New York, N.Y.) (2022)
Publication types: Journal Article
Maternal Ethanol Exposure-Induced Cardiac Fibrosis is Associated with Changes in TGF-β and SIRT1/FOXO3a Signaling in Male Rat Offspring: A Three-Month Follow-up Study.

Ethanol exposure during pregnancy induces cardiac fibrosis in the fetal heart.However, the mechanisms by which consumption of ethanol induces fibrotic changes are not known.Pregnant rats were received ethanol 4.5 g/kg bw once per day from the 7th day of pregnancy (gd7) throughout lactation.Our findings demonstrated that, area of fibrosis increased in cardiac tissue in the pups on both postnatal day twenty one (pn21) and postnatal day ninety (pn90) after prenatal and early postnatal period ethanol treatment compared with the controls.It was accompanied by a decline in the expression of sirt1 protein along with the elevation of foxo3a and tgf-β protein expressions which were determined by western blot.Overall, our data reveal that prenatal alcohol usage increase in fibrotic regions in the pup hearts possibly by regulating tgf-β, foxo3a and sirt1 protein levels.These are potential therapeutic molecular targets that can be modulated to protect heart against maternal ethanol exposure.

Journal: Cardiovascular toxicology (2022)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Qubit readout error mitigation with bit-flip averaging.

Quantum computers are becoming increasingly accessible and may soon outperform classical computers for useful tasks.However, qubit readout errors remain a substantial hurdle to running quantum algorithms on current devices.We present a scheme to more efficiently mitigate these errors on quantum hardware and numerically show that our method consistently gives advantage over previous mitigation schemes.Our scheme removes biases in the readout errors, allowing a general error model to be built with far fewer calibration measurements.Specifically, for reading outn-qubits, we show a factor of 2nreduction in the number of calibration measurements without sacrificing the ability to compensate for correlated errors.Our approach can be combined with, and simplify, other mitigation methods, allowing tractable mitigation even for large numbers of qubits.

Journal: Science advances (2021)
Publication types: Journal Article
Synthesis and application of CdS nanorods for LED-based photocatalytic degradation of tetracycline antibiotic.

With the rapid development of pharmaceutical industrialization, increased consumption of drugs and discharged sewage contains antibiotics that lead to water contamination.For this purpose, removal of antibiotics from aquatic environment is emphasizing the need to produce clean water using easy separable catalysts through photocatalytic water remediation and thus the semiconductor photocatalysts have presently gained fascinating unprecedented research attention.Herein, we present the synthesis of semiconductor cd s nanorods by a facile hydrothermal procedure using ethylene diamine as a coordinating agent.Then, we subsequently studied the photocatalytic activity of cd s nanorods under blue and white led light irradiation for the degradation of tetracycline antibiotic as a model compound.The light dependent photocatalytic activity of cd s nanorods demonstrated that cd s nanorods possess higher catalytic efficiency in presence of blue light compared to white light toward the photocatalytic degradation of tetracycline antibiotic.We have also studied the photocatalytic activity in presence of various light intensity.These cd s nanorods exhibited the highest tetracycline degradation efficacy of 95.6% within 60 min in presence of blue light (intensity: 200w/m2) without any supplementary oxygen sources during the degradation reaction.The photocatalytic mechanism of the tetracycline degradation has been elucidated by scavenging experiment.The experimental results indicate the formation of reactive oxygen species during photocatalytic degradation of tetracycline antibiotic.This work represents an alternative route to develop heterogeneous photocatalyst for antibiotics degradation due to the outstanding efficiency and stability of the cd s nanorods as well as easy separation through simple filtration method.It is anticipated that this work will shed light in the practical applications of cd s nanorods for environmental remediation through wastewater treatment.

Journal: Chemosphere (2022)
Publication types: Journal Article
Sleep disturbances in infants and young children following an acquired brain injury.

Study objectives sleep disturbances impact over half of older children and teens with acquired brain injury (abi) following critical care hospitalization but are underevaluated in infants and young children.Given the importance of sleep in brain development and healing after injury, we hypothesized sleep disturbances would be associated with worse neurodevelopmental outcomes in infants with abi.Methods we performed a retrospective cohort study of 68 children aged 2-32 months following critical care hospitalization for abi.The brief infant sleep questionnaire assessed sleep disturbances.Bayley scales of infant and toddler development, third edition and adaptive behavior assessment system, third edition assessed developmental and adaptive functioning outcomes, respectively.ttests compared sleep characteristics in infants with abi to historical healthy controls.Spearman's correlation evaluated relationships among sleep and outcomes.Multiple linear regression investigated relationships controlling for demographic and abi characteristics.Results compared to healthy controls, children with abi had shorter nighttime sleep duration (p= .01), longer daytime sleep duration (p< .001), and longer duration of nighttime awakenings (p< .001).Duration of night awakenings negatively correlated with bayley cognitive scores (spearman's correlation = -.40).Night awakenings negatively correlated with worse adaptive behavior assessment system, third edition general adaptive composite scores (spearman's correlation = -.42).When controlling for demographic and abi characteristics, ≥ 3 awakenings was significantly associated with worse adaptive behavior assessment system, third edition general adaptive composite (β = -11.3; 95% confidence interval = -19.2, -3.5).Conclusions sleep disturbances are associated with poorer outcomes in infants and toddlers after abi.Sleep is vital to recovery and a potentially modifiable target to improve outcomes.Citation klapp jm, hall ta, riley ar, williams cn.Sleep disturbances in infants and young children following an acquired brain injury.j clin sleep med.2022;18(10):2387-2395.

Journal: Journal of clinical sleep medicine : JCSM : official publication of the American Academy of Sleep Medicine (2022)
Publication types: Journal Article;Research Support, N.I.H., Extramural
Predicting ground reaction forces of human gait using a simple bipedal spring-mass model.

Aircraft design must be lightweight and cost-efficient on the condition of aircraft certification.In addition to standard load cases, human-induced loads can occur in the aircraft interior.These are crucial for optimal design but difficult to estimate.In this study, a simple bipedal spring-mass model with roller feet predicted human-induced loads caused by human gait for use within an end-to-end design process.The prediction needed no further experimental data.Gait movement and ground reaction force (grf) were simulated by means of two parameter constraints with easily estimable input variables (gait speed, body mass, body height).To calibrate and validate the prediction model, experiments were conducted in which 12 test persons walked in an aircraft mock-up under different conditions.Additional statistical regression models helped to compensate for bipedal model limitations.Direct regression models predicted single grf parameters as a reference without a bipedal model.The parameter constraint with equal gait speed in experiment and simulation yielded good estimates of force maxima (error 5.3%), while equal initial grf gave a more reliable prediction.Both parameter constraints predicted contact time very well (error 0.9%).Predictions with the bipedal model including full grf curves were overall as reliable as the reference.

Journal: Royal Society open science (2022)
Publication types: Journal Article
Social Camouflaging in Autistic and Neurotypical Adolescents: A Pilot Study of Differences by Sex and Diagnosis.

Camouflaging is a process through which individuals mask autistic traits.Studies suggest autistic females may camouflage more than autistic males.However, research has focused on adults and includes few comparisons between autistic and neurotypical individuals.This study compared levels of camouflaging by sex and diagnosis in autistic and neurotypical adolescents.Females reported higher overall levels of camouflaging when not accounting for age.When accounting for age, an age by diagnosis interaction effect emerged.This possible effect of age on camouflaging has implications for understanding how camouflaging behaviors develop and warrants further exploration.Differences also emerged on behaviors labeled as masking and assimilation, subcomponents of camouflaging, with females appearing more similar to their neurotypical peers on behaviors related to social awareness.

Journal: Journal of autism and developmental disorders (2020)
Publication types: Journal Article
Metagenome-assembled genomes recovered from the datasets of a high-altitude Himalayan hot spring Khirganga, Himachal Pradesh, India.

Khirganga, a pristine hot spring that lies in the parvati valley within the northern himalayas characterised with unique white colour microbial mat and divine water with healing abilities.Here, we report 41 metagenome-assembled genomes (mags) reconstructed from the microbial mat, sediment and water samples of hot spring passed through genome standards consortium (gsc) and minimum information of metagenome-assembled genome (mimag).

Journal: Data in brief (2021)
Publication types: Journal Article
Proinflammatory follicular helper T cells promote immunoglobulin G secretion, suppress regulatory B cell development, and correlate with worse clinical outcomes in gastric cancer.

Gastric cancer is one of the most common and aggressive malignancies.Both bacterial virulence factors and host chronic inflammation are thought to promote gastric cancer development.In this study, we investigated the potential involvement of follicular helper t cells in gastric cancer.Functions of follicular helper t subsets were examined in helicobacter pylori-infected gastric cancer patients and h.Pylori-infected but asymptomatic individuals.We found that the follicular helper t cells in gastric cancer individuals were skewed toward the th1 and th17 subsets compared to those in h.Pylori-infected but asymptomatic individuals.In a naive b cell-follicular helper t cell coculture, the th1-follicular helper t cells by themselves were ineffective at stimulating a robust antibody response, unlike the th2-follicular helper t and th17-follicular helper t cells.However, th1-follicular helper t cells significantly promoted the immunoglobulin g response in collaboration with other follicular helper t subsets, through the secretion of interferon gamma.We also found that th1-follicular helper t cells suppressed the development of interleukin-10+regulatory b cells, a cell type previously thought to protect h.Pylori-infected individuals from tissue damage.In addition, the frequency of th1-follicular helper t cells in gastric cancer patients was negatively correlated with the disease-free survival of gastric cancer patients after tumor resection.These results suggested that dysregulation of follicular helper t subsets in gastric cancer patients, characterized by increased th1-follicular helper t cells, contributed to inflammation and tumor development.

Journal: Tumour biology : the journal of the International Society for Oncodevelopmental Biology and Medicine (2017)
Publication types: Journal Article
Intraoperative Comparative Femoral Rotation Imaging: Do not Overlook Parallax.

To investigate the degree of error due to parallax during intraoperative rotational imaging involving the distal femur.Methods twelve, fresh-frozen, lower-extremity cadaveric specimens were studied.The limbs were positioned supine and rotated until the posterior femoral condyles were superimposed using a c-arm.The c-arm was then repositioned to place the femoral condyles at the anterior and posterior margins of the image intensifier.The rotation necessary to resuperimpose the femoral condyles due to parallax was recorded.A second c-arm was then used from the contralateral side to simulate the rotational imaging technique to determine the magnitude and directionality of combined parallax.Results all 12 specimens demonstrated parallax, resulting in rotational discrepancies.Compared with central field of view alignment, the mean rotational discrepancy was 5.6 and 5.5 degrees for anterior and posterior positions, respectively.Contralateral imaging resulted in an additive effect with rotational differences of 9.0 and 12.6 degrees for bilateral anterior and posterior positions, respectively.Conclusions parallax causes rotational discrepancies with fluoroscopic imaging of the distal femur when the posterior femoral condyles are off-center in the imaging field of view.If femoral condyles are not centered when obtaining intraoperative rotational imaging of the uninjured and injured femurs, parallax can result in potentially clinically significant rotational deformity even if the femurs seem perfectly matched at the conclusion of surgery.We recommend perfectly centering of the posterior femoral condyles in the imaging field of view when obtaining lateral images of the distal femur to prevent this potentially overlooked contribution to malrotation.

Journal: Journal of orthopaedic trauma (2022)
Publication types: Journal Article