Miracle-dz/UniFAR-FTUs huggingface dataset:
Comprehensive analysis of tumor mutation burden and immune microenvironment in gastric cancer

Abstract Tumor mutation burden (TMB) was a promising marker for immunotherapy. We aimed to investigate the prognostic role of TMB and its relationship with immune cells infiltration in gastric cancer (GC). We analyzed the mutation landscape of all GC cases and TMB of each GC patient was calculated and patients were divided into TMB-high and TMB-low group. Differentially expressed genes (DEGs) between the two groups were identified and pathway analysis was performed. The immune cells infiltration in each GC patient was evaluated and Kaplan–Meier analysis was performed to investigate the prognostic role of immune cells infiltration. At last, hub immune genes were identified and a TMB prognostic risk score (TMBPRS) was constructed to predict the survival outcome of GC patients. The relationships between mutants of hub immune genes and immune infiltration level in GC was investigated. We found higher TMB was correlated with better survival outcome and female patients, patients with T1-2 and N0 had higher TMB score. Altogether 816 DEGs were harvested and pathway analysis demonstrated that patients in TMB-high group were associated with neuroactive ligand–receptor interaction, cAMP signaling pathway, calcium signaling pathway. The infiltration of activated CD4+ memory T cells, follicular helper T cells, resting NK cells, M0 and M1 macrophages and neutrophils in TMB-high group were higher compared than that in TMB-low group and high macrophage infiltration was correlated with inferior survival outcome of GC patients. Lastly, the TMBPRS was constructed and GC patients with high TMBPRS had poor prognosis.
Toward a humanized mouse model of Pneumocystis pneumonia

Pneumocystis is an important opportunistic fungus that causes pneumonia in children and immunocompromised individuals. Recent genomic data show that divergence of major surface glycoproteins may confer speciation and host range selectivity. On the other hand, immune clearance between mice and humans is well correlated. Thus, we hypothesized that humanize mice may provide information about human immune responses involved in controlling Pneumocystis infection. CD34-engrafted huNOG-EXL mice controlled fungal burdens to a greater extent than nonengrafted mice. Moreover, engrafted mice generated fungal-specific IgM. Fungal control was associated with a transcriptional signature that was enriched for genes associated with nonopsonic recognition of trophs (CD209) and asci (CLEC7A). These same genes were downregulated in CD4-deficient mice as well as twins with bare lymphocyte syndrome with Pneumocystis pneumonia.
Guilt, shame, and postpartum infant feeding outcomes: A systematic review

Abstract Negative maternal affect (e.g., depression and anxiety) has been associated with shorter breastfeeding duration and poorer breastfeeding intention, initiation, and exclusivity. Other affective states, including guilt and shame, have been linked with formula feeding practice, though existing literature has yet to be synthesised. A narrative synthesis of quantitative data and a framework synthesis of qualitative and quantitative data were conducted to explore guilt and/or shame in relation to infant feeding outcomes. Searches were conducted on the DISCOVER database between December 2017 and March 2018. The search strategy was rerun in February 2020, together yielding 467 studies. The study selection process identified 20 articles, published between 1997 and 2017. Quantitative results demonstrated formula feeders experienced guilt more commonly than breastfeeding mothers. Formula feeders experienced external guilt most commonly associated with healthcare professionals, whereas breastfeeding mothers experienced guilt most commonly associated with peers and family. No quantitative literature examined shame in relation to infant feeding outcomes, warranting future research. The framework synthesis generated four distinct themes which explored guilt and/or shame in relation to infant feeding outcomes: ‘underprepared and ineffectively supported’, ‘morality and perceived judgement’ (breastfeeding), ‘frustration with infant feeding care’ and ‘failures, fears and forbidden practice’ (formula feeding). Both guilt and shame were associated with self‐perception as a bad mother and poorer maternal mental health. Guilt and shame experiences were qualitatively different in terms of sources and outcomes, dependent on infant feeding method. Suggestions for tailored care to minimise guilt and shame, while supporting breastfeeding, are provided.
Gas phase equilibrium limitations on the vapor–liquid–solid growth of epitaxial silicon nanowires using SiCl_4

Epitaxially oriented silicon nanowires (SiNWs) were grown on (111) Si substrates by the vapor–liquid–solid technique in an atmospheric-pressure chemical vapor deposition (APCVD) system using Au as the catalyst and SiCl_4 as the source gas. The dependencies of SiNW growth rate on the growth temperature and SiCl_4 partial pressure (P_SiCl4) were investigated, and the experimental results were compared with calculated supersaturation curves for Si obtained from a gas phase equilibrium model of the SiCl_4–H_2 system. The SiNW growth rate was found to be weakly dependent on temperature but strongly dependent on the P_SiCl4, exhibiting a maximum value qualitatively similar to that predicted from the equilibrium model. The results indicate that SiNW growth from SiCl_4 is limited by gas phase chemistry and transport of reactant species to the growth surface under APCVD conditions. The experimental results are discussed within the context of a gas phase mass transport model that takes into account changes in equilibrium partial pressure due to curvature-related Gibbs–Thomson effects.
FUNDAMENTAL SCALING EFFECTS OF ACETYLENE AND NATURAL GAS FREE-JET FLAMES

The aerodynamic and turbulent structures of combusting, partially premixed free-jet flames, with varying size and for different fuels at constant equivalence ratio, are compared. The first fuel, natural gas, produced predominantly blue flames and was investigated using laser Doppler anemometry measuring techniques for three round-jet exit nozzle diameters to a distance X = 40 diameters downstream. Each jet had the same exit velocity, which was limited only by the blowoff limit. A similar set of experiments was repeated with acetylene, a fuel of higher calorific value producing highly radiative yellow flames. Constant exit velocities were maintained for all cases; in this case the higher flame speed of acetylene allowed higher values of exit velocity to be used. The natural gas flames were then revisited and the flow was seeded with fine coal particles of constant mean diameter and their effect on the flow dynamics was explored using particle image velocimetry for acetylene jet flames it was found that mean velocities scale to X/D = 10, whereas fluctuating velocities are seen to increase across the jet from just beyond the nozzle exit. Normalized flame length and potential core decrease with increasing scale. Self-similarity was seen for mean velocity and different nozzle diameters, less so for fluctuating velocities. Relaminarization of the flames occurred between X/D = 5 and 10. Compared to acetylene, natural gas flames produce self-similarity to greater distances downstream due to longer flame lengths. They also have lower fluctuating velocity levels and exhibit only a slight increase in large-scale turbulence. Comparison of results with other studies shows that induced turbulence into the jet at small scale may be needed to simulate larger scale systems. Finally, the addition of fine coal particles to natural gas flames is shown to delay vorticity formation and mixing, the latter increasing with nozzle diameter.
Cogstate Brief Battery: Cognition and the feigning of cognitive impairment in chronic pain

Abstract Chronic pain (CP) is often associated with cognitive impairment. The Cogstate Brief Battery (CBB), a computerized assessment battery, has been studied in several neuropsychiatric disorders but not in CP. Since feigning of cognitive impairment is common in CP, the current study aimed to assess the CBB’s utility in differentiating CP patients (n = 64) from healthy participants (n = 33), as well as to assess the effect of simulating cognitive impairment by CP patients on performance in the battery. CP outpatients were randomly assigned to one of two groups: (a) Patients performing the CBB to the best of their ability. (b) Patients simulating cognitive impairment. Independent-samples t-tests indicated that three of four CBB tasks successfully differentiated CP patients from matched healthy controls. Additionally, an analysis of covariance (ANCOVA) indicated that CP patients who simulated cognitive impairment performed more poorly in all four CBB tasks, with the detection task having the strongest discrimination capacity. This is the first study to point toward the usefulness and sensitivity of the CBB for assessment of cognition and detection of feigned cognitive impairment in CP. Further studies are required to validate these preliminary findings and assess the CBB’s utility in daily clinical practice.
Affinity for Thyroid Hormone and Estrogen Receptors of Hydroxylated Polybrominated Diphenyl Ethers

The affinity for thyroid hormone receptor (TR) of polybromodiphenyl ethers (PBDEs) and hydroxylated PBDEs was examined. 4-Hydroxy-2,2',3,4',5-pentabromodiphenyl ether (4-OH-BDE-90) and 3-hydroxy-2,2',4,4'-tetrabromodiphenyl ether (3-OH-BDE-47) markedly inhibited the binding of triiodothyronine (1×10-10 M) to TR in the concentration range of 1×10-6-1×10-4 M. 2,3,4,5,6-Pentabromophenol (PBP) also showed an inhibitory effect at 1×10-5-1×10-4 M. However, 2,2',3,4,4',5'-hexabromodiphenyl ether (BDE-138), decabromodiphenyl ether (DBDE), 4-methoxy-2,2',3,4',5-pentabromodiphenyl ether (4-MeO-BDE-90), 4'-hydroxy-2,2',4,5'-tetrabromodiphenyl ether (4'-OHBDE-49), 4-hydroxy-2,2',3,4'-tetrabromodiphenyl ether (4-OH-BDE-42), 4'-hydroxy-2,2',4-tribromodiphenyl ether (4'-OH-BDE-17), 3'-hydroxy-2,4-dibromodiphenyl ether (3'-OH-BDE-7), 2,4,6-tribromophenol (TBP) and tetrabromohydroquinone (TBHQ) did not show affinity for TR. In contrast, 4'-OH-BDE-17 and 3'-OH-BDE-7 exhibited estrogenic activity in estrogen-responsive reporter assay using MCF-7 cells at the concentration of 1×10-5 M. However, adjacent bromo substitution of 3- or 4-hydroxylated PBDEs markedly decreased the estrogenic activity. These results suggest that hydroxylated PBDEs act as thyroid hormone-like agents, as well as estrogens, that a 4- or 3-hydroxyl group in PBDEs is essential for thyroid hormonal and estrogenic activities, and that adjacent dibromo substitution favors thyroid hormonal activity, but not estrogenic activity.
Inter-rater Reliability of the McKenzie Method of Mechanical Diagnosis and Therapy for the Provisional Classification of Low Back Pain in Adolescents and Young Adults

ABSTRACT Objective To investigate the inter-rater reliability of Mechanical Diagnosis and Therapy (MDT)-trained Diplomats in classifying adolescents and young adults with lumbar pain. Methods Forty-three participants (mean age 15 ± 2 years) with lumbar pain, with or without lower extremity symptoms, were assessed simultaneously by three MDT Diploma holders and classified into one of three groups: 1) Derangement, 2) Dysfunction, 3) Postural/OTHER. Inter-rater reliability was calculated using the Fleiss kappa statistics with 95% confidence intervals (CI). Analyses were repeated with the younger (11 to 15 years old) and older (16 to 21 years old) age groups. Results There was moderate reliability (Fleiss kappa = 0.50, 95% CI = 0.45 to 0.54) for the entire sample, which was statistically significant (p < 0.001). There was good reliability in older participants (Fleiss kappa = 0.63, 95% CI = 0.57 to 0.70), but poor reliability in younger participants (Fleiss kappa = 0.33, 95% CI = 0.27 to 0.39). There was 100% agreement in classifications among assessors for 70% of participants. Discussion The MDT system has moderate reliability when classifying lumbar pain in adolescents and young adults. Future reliability studies may include a balanced group for classifications or a second session.
Comparison of circular stapling, triangulating stapling and T-shape stapling for cervical anastomosis with minimally invasive esophagectomy

Background The triangulating stapling (TST) and T-shape stapling (TS) methods have been proposed to decrease the incidence of anastomotic leakage after esophagectomy, but few studies have compared them to the circular stapling technique (CS). This retrospective study aimed to compare the efficacy and safety of three cervical anastomosis methods after esophagectomy. Methods Squamous cell carcinoma patients who underwent minimally invasive esophagectomy (MIE) with CS, TST or TS anastomosis between April 2010 and June 2012 were recruited. Their clinical characteristics and short-term outcome were analyzed. Kaplan-Meier analyses compared with log-rank test were used to calculate the effect of the three types of cervical anastomosis on overall survival (OS) and disease-free survival (DFS). Results The incidence of anastomotic leakage was 21.8% in the CS group, 7.7% in the TS group and 11.9% in the TST group (P=0.029). There were significant differences in the incidence of gastroesophageal reflux among the three groups (P<0.001). Rates of anastomotic stenosis, pulmonary infection, chylothorax and hoarseness were not different among the groups. There were significant differences in anastomotic time, operation time and hospitalization time (all P<0.001), but there was no significant difference in albumin content at 1 month after operation (P=0.226). There was no differences in long-term surgical effects of the three types of anastomosis Conclusions Cervical esophagogastric anastomosis by TST or TS can be considered feasible and safe and with improved short-term outcome.
Higher Levels of Triglyceride, Fatty Acid Translocase, and Toll-Like Receptor 4 and Lower Level of HDL-C in Pregnant Women with GDM and Their Close Correlation with Neonatal Weight

Objectives: In this study, we aimed to compare the levels of maternal blood lipids, placental and venous blood lipid transporters, and inflammatory factor receptors in pregnant women with and without gestational diabetes mellitus (GDM). We also aimed to figure out the relationship between these values and neonatal weight. Methods: Fifty pregnant women with GDM under blood glucose control belong to the case group, and 50 pregnant women with normal glucose tolerance in concurrent delivery belong to the control group. Fasting venous blood of these pregnant women was taken 2 weeks before delivery, and umbilical cord blood was collected after delivery. The levels of triglyceride (TG), serum total cholesterol, low-density lipoprotein cholesterol, and high-density lipoprotein cholesterol (HDL-C) in maternal blood and umbilical cord blood were tested in the laboratory department of our hospital. The level of toll-like receptor 4 (TLR4) in serum of umbilical veins was detected by the double-antibody sandwich ELISA. Western blot and RT-PCR were used to detect the protein and mRNA expressions of TLR4, LPL, and FAT/CD36 in the placenta. Results: The level of TG in maternal blood in the case group was remarkably higher than that in the control group, which was opposite to the level of HDL-C. In the umbilical cord blood of women with GDM, the expression of TLR4 increased and was closely correlated with neonatal weight. In the placenta of women with GDM, the expressions of FAT/CD36 and TLR4 increased, and both of them were closely correlated with neonatal weight. Besides, TLR4 in umbilical cord blood increased and was closely correlated with neonatal weight. Although the expression of LPL in the placenta decreased, it had no obvious correlation with neonatal weight. Conclusions: TG in maternal blood, TLR4 in the placenta and umbilical cord blood, and FAT/CD36 in the placenta were positively correlated with neonatal weight. However, HDL-C in maternal blood was negatively correlated with neonatal weight. Although the expression of LPL in the placenta reduced due to GDM, it had no correlation with neonatal weight.
Efficient expression of concatenated α1β2δ and α1β3δ GABAA receptors, their pharmacology and stoichiometry

GABAA receptors containing δ‐subunits are notorious for being difficult to study in vitro due to heterogeneity of expressed receptor populations and low GABA‐evoked current amplitudes. Thus, there are some published misconceptions and contradictory conclusions made regarding the pharmacology and stoichiometry of δ‐containing receptors. The aim of this study was to obtain robust homogenous expression of α1βδ receptors for in‐depth investigation.
Genotype and phenotype correlation in a cohort of Chinese congenital hypothyroidism patients with DUOX2 mutations

Background This study aimed to explore the relationship between the phenotype and genotype of congenital hypothyroidism (CH) caused by dual oxidase 2 (DUOX2) mutation in Chinese children, and to investigate the genetic causes of permanent and transient hypothyroidism through next-generation genetic testing technology and long-term clinical follow-up data. Methods We recruited 61 patients with thyroid stimulating hormone (TSH) levels of >10 mIU/mL during newborn screening, clinical diagnosis of CH, and L-thyroxine (L-T4) oral treatment within 1 month of birth; they were followed up until the present. All CH infants and their parents were genotyped using whole-exome sequencing (WES); DUOX2 variants were detected in 20 infants, and the longitudinal prognosis, genotype, and phenotype correlations were analyzed. Results Biallelic DUOX2 mutations were detected in 20 participants. All of them were born full term. All patients were treated with L-T4 when diagnosed with CH; 9 of them stopped L-T4 eventually before 3 years old; and 2 were treated with a reduced dose of L-T4 (12.5 µg per day). The others were still treated with L-T4 at a dose of 37.5–87.5 µg per day. Of these 20 participants, 5 carried an R1110Q variant and 5 carried K530X variants. A total of 7 novel variants were discovered in our cohort. The variants carried in transient CH patients were located extracellularly and not near the functional domain. Conclusions Most CH patients with DUOX2 mutations were those with transient or subclinical CH. The R1110Q, R885L, and K530X were the most common variants in our Chinese cohort. The R1110Q and K530X variants may play a founder effect in the transient CH. The R885L variant may play a benign role in transient CH. Intracellular variants or those near the functional domain may cause permanent CH.
The accuracy of MRI in the diagnosis of anterior cruciate ligament injury

Background Anterior cruciate ligament (ACL) injury can cause damage to the meniscus and articular cartilage, and may even lead to osteoarthritis. This study aimed to analyze the accuracy and feasibility of magnetic resonance imaging (MRI) imaging signs in the diagnosis of knee joint ACL injury. Methods A total of 78 patients admitted to our hospital from June 2018 to October 2019 with highly suspected ACL injury were selected for this prospective study. We used MRI and arthroscopy to diagnose the ACL injuries, and the results of MRI and arthroscopy, as well as the value of MRI in diagnosing ACL injury, were compared. Results Among the 78 participants, 66 cases were diagnosed with ACL injury (28 with complete tear, 38 with partial tear), and 12 were normal according to arthroscopy. Among the 66 cases with ACL injury, 63 (95.45%) were confirmed by MRI detection. The sensitivity, specificity, and accuracy of MRI in the diagnosis of ACL injury were 95.45% (63/66), 91.67%, and 94.87%, respectively. The accuracy of MRI in the diagnosis of complete and partial tears were 92.86% and 94.74%, respectively. Among the four direct MRI signs of ACL injury, the differences in interruption of ACL continuity, thickening and edema, and abnormal walking were statistically significant (P<0.05). Among the 8 indirect MRI signs, all showed high specificity and low sensitivity, and which the specificity of posterior cruciate ligament index, Notch sign, meniscus exposure sign of posterior ankle, and lateral collateral ligament monolayer display showed higher specificity (P<0.05). Conclusions Examination with MRI offers high accuracy in the diagnosis of ACL injury, and has good consistency with arthroscopic diagnosis, which can provide reliable guidance for the selection and formulation of clinical surgery plans, and might be used as the first choice for the non-traumatic diagnosis of ACL injury.
Liquid state theory of the structure and phase behaviour of polymer-tethered nanoparticles in dense suspensions, melts and nanocomposites

We have studied the structure and phase behaviour of spherical nanoparticles grafted with a modest number of polymer tethers in the dense suspension and pure melt states, and dissolved in a homopolymer matrix, using the polymer reference interaction site model integral equation theory. In the absence of a polymer matrix, fluids of tethered nanoparticles exhibit strong concentration fluctuations indicative of aggregate formation and/or a tendency for microphase separation as the total packing fraction and/or nanoparticle attraction strength increase. For nanoparticles of core diameter twice that of the monomer, carrying one, two and four tethers, the microphase spinodal temperature grows roughly as a power-law function of packing fraction. As the number of polymer tethers increases, the microphase spinodal curve shifts to lower temperatures due to steric shielding of the nanoparticle core. In the presence of a homopolymer matrix, the microphase spinodal curve of single-tethered particles exhibits both dilution-like and depletion-like features and a non-monotonic dependence of the spinodal temperature on matrix chain length. As the number of tethers is increased, the microphase curves become more dilution-like and the effect of matrix degree of polymerisation, particle size and tether length on the apparent spinodal temperature diminishes.
Comparative pharmacokinetics of metronidazole in healthy and Trichomonas gallinae infected pigeons (Columba livia, var. domestica)

ABSTRACT 1. This study investigated the pharmacokinetics of metronidazole after intravenous (i.v.) and oral administration to healthy and experimentally Trichomonas gallinae-infected pigeons, and determined the in vitro antiprotozoal activity of metronidazole against T. gallinae. 2. Twelve pigeons which were experimentally infected to T. gallinae and twelve healthy pigeons received metronidazole at the dose of 25 mg/kg by oral or i.v. administration. Serial blood sampling was used for pharmacokinetic analysis. The metronidazole minimum lethal concentration (MLC) and the concentration killing 50% of the trophozoites (LC50) in the culture media were determined. 3. In vitro data showed that the 24 h LC50 and MLC of metronidazole were 0.31 and 25 µg/ml, respectively. In vivo results showed no statistical differences between pharmacokinetics in infected and non-infected pigeons for both routes of administration. The area under the curve was statistically higher after the i.v. administration in both infected and healthy pigeons. The mean oral bioavailability was similar in the infected (83.8%) and the healthy (81.5%) birds. 4. In conclusion, the pharmacokinetics of metronidazole in pigeons was not affected by experimentally-induced trichomoniasis. Despite in vitro susceptibility testing, which showed probable resistance of the isolated T. gallinae to metronidazole, five-day oral treatment of infected pigeons with 25 mg/kg metronidazole twice a day resulted in total eradication of trophozoites recovered in crop lavage of infected birds.