Miracle-dz/UniFAR-FTUs huggingface dataset:
Specific Biomarker Expression Patterns in the Diagnosis of Residual and Recurrent Endometrial Precancers After Progestin Treatment

Background: Conservative management with progestin is a treatment option for atypical hyperplasia (AH). However, pathologic diagnosis of residual/recurrent lesions is often problematic because of the profound morphologic changes induced by progestin and the lack of established diagnostic criteria for progestin-treated residual AH. Methods: We conducted a longitudinal study of 265 endometrial biopsies from 54 patients with a history of AH on progestin therapy. Patient outcomes were divided into 3 categories after morphologic review and immunohistochemical staining with phosphatase and tensin homolog (PTEN) and paired box 2 (PAX2): (1) persistent or residual disease; (2) recurrent disease; (3) complete response. All specimens were classified into 3 categories based on morphology: (1) persistent/recurrent disease (nonresponse), (2) morphologically uncertain response, (3) optimally treated (complete response). The staining patterns of PTEN/PAX2 were tracked over time in individual patients and correlated with morphologic findings before and after progestin therapy. Results: Our data showed that aberrant expression patterns of PTEN and/or PAX2 were identified in 48 (88.9%) of the 54 primary biopsies and persisted in persistent/recurrent AH across serial endometrial biopsies (n=99, P<0.00001), while normal PTEN and PAX2 expressions were consistently observed in optimally treated cases (n=84, P<0.00001). More importantly, follow-up biopsies that showed a morphologically uncertain response but a PTEN/PAX2 expression pattern identical to the initial biopsy were significantly correlated with persistent or recurrent disease (n=18, P=0.000182), as evidenced by areas with morphologic features diagnostic of AH on subsequent biopsy. Conclusions: Biomarker PTEN/PAX2 signatures offer a valuable diagnostic aid to identify residual AH in progestin-treated endometrial samples for which the biomarker status from preprogestin treated AH is known. The findings of this study are promising for a possible future change of diagnostic practice.
Maximal Axial Vertebral Rotation in Adolescent Idiopathic Scoliosis: Is the Apical Vertebra the Most Rotated?

Study Design: Retrospective cross-sectional study. Objectives: It is generally believed that the apical vertebra has the largest axial rotation in adolescent idiopathic scoliosis. We investigated the relationship between apical axial vertebral rotation (apicalAVR) and maximal axial vertebral rotation (maxAVR) in both major and minor curves using biplanar stereo-imaging. Methods: EOS 2D/3D biplanar radiograph images were collected from 332 patients with adolescent idiopathic scoliosis (Cobb angle range 10°-122°, mean age 14.7 years). Based on the X-ray images, with the help of 3D full spine reconstructions Cobb angle, curvature level, apicalAVR and maxAVR were determined. These parameters were also determined for minor curves in Lenke 2, 3, 4, 6 type patients. Maximal thoracic rotation and maximal thoracolumbar/lumbar rotation were calculated. Statistical analysis was performed with descriptive statistics, Shapiro-Wilk test, and Wilcoxon signed-rank test. Results: The apical vertebrae were the most rotated vertebra in only 40.4% of the major curves, and 31.7% in minor curves. MaxAVR significantly exceeded apicalAVR values in the major curves (P < .001) as well as in minor curves (P < .001). The 2 parameters differed significantly in each severity group and Lenke type. Conclusions: The apical vertebrae were not the most rotated vertebra in more than half of cases investigated indicating that apicalAVR and maxAVR should be considered as 2 distinct parameters, of which maxAVR fully describes the axial dimension of scoliosis. Furthermore, the substitution of maxAVR for the apicalAVR should be especially avoided in double and triple curves, as the apical vertebra was even less commonly the most rotated in minor curves.
Differential utilization of CD4 by transmitted/founder and chronic envelope glycoproteins in a MSM HIV-1 subtype B transmission cluster.

OBJECTIVE HIV-1 transmission leads to a genetic bottleneck, with one or a few variants of the donor quasispecies establishing an infection in the new host. We aimed to characterize this bottleneck in more detail, by comparing the properties of HIV envelope glycoproteins from acute and chronic infections within the particular context of a male-to-male transmission cluster. DESIGN We compared the genotypic and phenotypic properties of envelope glycoproteins from viral variants derived from five study participants from the same transmission cluster. METHODS We used single-genome amplification to generate a collection of full-length env sequences. We then constructed pseudotyped viruses expressing selected Env variants from the quasispecies infecting each study participant and compared their infectivities and sensitivities to various entry inhibitors. RESULTS The genotypic analyses confirmed the genetic bottleneck expected after HIV transmission, with a limited number of variants identified in four study participants during acute infection. However, the transmitted sequences harbored no evident common signature and belonged to various genetic lineages. The phenotypic analyses revealed no difference in infectivity, susceptibility to the CCR5 antagonist maraviroc, the fusion inhibitor enfurvitide or type-I interferon between viruses from participants with acute and chronic infections. The key property distinguishing transmitted viruses was a higher resistance to soluble CD4, correlated with greater sensitivity to occupation of the CD4 receptor by the anti-CD4 antibodies LM52 and SK3. CONCLUSION These results suggest that envelope glycoproteins from transmitted/founder viruses bind CD4 less efficiently than those of viruses from chronic infections.
The use of internal otolith morphometrics for identification of haddock (Melanogrammus aeglefinus) stocks on Georges Bank

Otoliths are crystalline structures composed of calcium carbonate and are ideal structures for use in fi sh stock identifi cation, containing a range of measurable characteristics including linear and shape morphometrics, optical density, and microstructural zonation and growth patterns, and elemental constituents (Ihssen et al., 1981; Campana and Neilson, 1985; Pawson and Jennings, 1996). Otoliths grow throughout the life of fi sh, are metabolically inert, and are typically available as a historical time series because of routine age and growth assessments (Campana and Neilson, 1985; Campana and Casselman, 1993). Linear and shape morphometrics of otoliths have been widely used for fi sh stock identifi cation (e.g. Messieh et al., 1989; Dawson, 1991; Smith, 1992; Campana and Casselman, 1993; Friedland and Reddin, 1994), although their use has been questioned because of withinstock differences in sex, age, and yearclass variation (Castonguay et al., 1991; Begg and Brown, 2000). Moreover, otolith morphometrics have been found to be strongly correlated with growth, which infl uences development of otolith crystalline microstructure (Smith, 1992; Campana and Casselman, 1993). Stock defi nitions based on differences in otolith structure, therefore, depend not only on differential growth rates, but on the consistency of the environment integrated over the life history of fi sh in each stock (Campana and CasThe use of internal otolith morphometrics for identifi cation of haddock (Melanogrammus aeglefi nus) stocks on Georges Bank
Variations in Callus Formation from Seeds in Japonica, Indica, their Hybrids, and Large Grain Varieties in Rice

On the culture media differing in the concentration of mineral microelements (B, Mn, Zn, I, Mo, Cu and Co), japoleica varieties except for Somewake and Daikoku 1 generally exhibited high abilities of callus formation. Indica and large grain varieties (assumed to be javanica type), japonica-indica hybrids, however, showed relatively poor and varying abilities of callus formation, especially on the mediurm with reduced mineral microelements. These results suggest that there may be different requirerments for the concentration of mineral microelements in callus formation among ecospecies and hybrids. From a comparison between Murasaki-Daikoku and Daikoku 1 having the same d-1 gene, it was presumed that the d-1 gene would not directly affect the callus formation, and some background genes, i. e. the suppressors may relate with the depresssion of callus formation. Likewise, it appears that semidwarf genes in Dee-geo-woo-gen and Taichung native 1 would not also suppress the calus formation. Slight depressions in many japonica-indica hybrids and IR-8, therefore, were attributed to some background genes, i. e. the sup-pressors of callus formation other than the semi-dwarf genes. Such suppressors appeared to occur most frequently in inedica and large grain varieties. Variations on morphological appearance of callus in japoleica, indica, their hybrids and large grain varieties were observed. The calluses of japonica and large grain varieties tended to be friable, those of japonica-iledica hybrids compact and those of indica intermediate. Diversities from the expected callus formation, i. e normal plant growth, white hairs, root cluster, white region and root-like structures were liable to occur most frequently in the hybrids. Necrosis and/or brownish color of calius tissues were likely to occur in the varieties which showed the reduced ability of callus formation.
The Wide Spectrum of COVID-19 Clinical Presentation in Children

Background: Ten months after its appearance in December 2019, SARS-CoV-2 has infected more than 25 million patients worldwide. Because children were first identified as potential spreaders of the virus, schools were closed in several countries. However, it rapidly became evident that the number of hospitalized children infected by SARS-CoV-2 was dramatically lower than that of adults. To date, only hypotheses have been raised to explain this difference, so it is of great importance to describe the presentation of this disease among children. Here, we describe a wide spectrum of COVID-19 manifestation in children in a dedicated pediatric unit in France. Methods: Patients hospitalized with COVID-19 who were diagnosed on the basis of either positive SARS-CoV-2 RT-PCR in nasopharyngeal swabs and/or typical aspects in chest-computed tomography (CT) were included between March and May 2020 in Paris. Results: Twenty-three patients were included on the basis of positive RT-PCR (n = 20) and/or typical aspects in CT (n = 4). The median age was 4.9 years [0.1–17.6]. Patients were grouped by age (<2 years old: n = 14, 61%; 2–10 years old: n = 2, 9%; >10 years old: n = 7, 30%). Overweight or obesity was reported in only three patients. At presentation, the most frequent symptom in the overall cohort was fever (n = 18, 78%), followed by acute rhinitis (n = 9, 64%) and cough (n = 7, 50%) in the under 2-year-old group and cough (n = 4, 57%), fatigue, dyspnea and abdominal pain (n = 3, 43% each) in the over 10-year-old group. Five patients required ICU treatment, four of whom were aged >10 years, two presented with acute myocarditis, and two were sickle cell disease patients who presented with acute chest syndrome. Discussion and conclusion: The youngest patients seem to present milder forms of COVID-19 without the need for ICU treatment and with a shorter length of hospitalization. More severe evolutions were observed in teenagers, with, however, favorable outcomes. Given the context of closed schools and confinement, the infection of these children suggests intra-familial transmission that needs to be further assessed. This description might help to understand the intriguing differences in COVID-19 severity across age-classes.
Effects of Human Milk Oligosaccharides on the Adult Gut Microbiota and Barrier Function

Human milk oligosaccharides (HMOs) shape the gut microbiota in infants by selectively stimulating the growth of bifidobacteria. Here, we investigated the impact of HMOs on adult gut microbiota and gut barrier function using the Simulator of the Human Intestinal Microbial Ecosystem (SHIME®), Caco2 cell lines, and human intestinal gut organoid-on-chips. We showed that fermentation of 2’-O-fucosyllactose (2’FL), lacto-N-neotetraose (LNnT), and combinations thereof (MIX) led to an increase of bifidobacteria, accompanied by an increase of short chain fatty acid (SCFA), in particular butyrate with 2’FL. A significant reduction in paracellular permeability of FITC-dextran probe was observed using Caco2 cell monolayers with fermented 2’FL and MIX, which was accompanied by an increase in claudin-8 gene expression as shown by qPCR, and a reduction in IL-6 as determined by multiplex ELISA. Using gut-on-chips generated from human organoids derived from proximal, transverse, and distal colon biopsies (Colon Intestine-Chips), we showed that claudin-5 was significantly upregulated across all three gut-on-chips following treatment with fermented 2’FL under microfluidic conditions. Taken together, these data show that, in addition to their bifidogenic activity, HMOs have the capacity to modulate immune function and the gut barrier, supporting the potential of HMOs to provide health benefits in adults.
Clinical characteristics and risk factors for coronavirus disease 2019 (COVID-19) among patients under investigation in Thailand

To manage coronavirus disease 2019 (COVID-19), a national health authority has implemented a case definition of patients under investigation (PUIs) to guide clinicians’ diagnoses. We aimed to determine characteristics among all PUIs and those with and without COVID-19. We retrospectively reviewed clinical characteristics and risk factors for laboratory-confirmed COVID-19 cases among PUIs at a tertiary care center in Bangkok, Thailand, between March 23 and April 7, 2020. Reverse transcription-polymerase chain reaction for SARS-CoV-2 RNA was performed. There were 405 evaluable PUIs; 157 (38.8%) were men, with a mean age ± SD of 36.2 ± 12.6 years. The majority (68.9%) reported no comorbidities. There were 53 (13.1%) confirmed COVID-19 cases. The most common symptoms among those were cough (73.6%), fever (58.5%), sore throat (39.6%), and muscle pain (37.4%). Among these patients, diagnoses were upper respiratory tract infection (69.8%), viral syndrome (15.1%), pneumonia (11.3%), and asymptomatic infection (3.8%). Multivariate analysis identified close contact with an index case (OR, 3.49; 95%CI, 1.49–8.15; P = 0.004), visiting high-risk places (OR, 1.92; 95%CI, 1.03–3.56; P = 0.039), productive cough (OR, 2.03; 95%CI, 1.05–3.92; P = 0.034), and no medical coverage (OR, 3.91; 95%CI, 1.35–11.32; P = 0.012) as independent risk factors for COVID-19 among the PUIs. The majority had favorable outcomes, though one (1.9%) died from severe pneumonia. COVID-19 was identified in 13% of PUIs defined per a national health authority’s case definition. History of contact with a COVID-19 patient, visiting a high-risk place, having no medical coverage, and productive cough may identify individuals at risk of COVID-19 in Thailand.
Gel Volume Near the Critical Point of Binary Mixture Isobutyric Acid–Water

The volume of a cylindrical polyacrylamide gel was measured when immersed in a binary mixture of isobutyric acid–water at different temperatures and weight fractions of isobutyric acid. Near the upper critical solution temperature of the binary mixture, the curve for gel volume vs. isobutyric acid weight fraction has a shoulder or a peak near the critical weight fraction. On the other hand, in a region away from the critical temperature, the gel volume decreased monotonically with increasing isobutyric acid weight fraction. The cloud point temperature of the binary mixture inside the gel was lower than that outside the gel. Thermodynamic description for the gel in the critical mixture is derived on the basis of the Ising model. By the description, the experimental results are explained consistently. The theoretical analysis shows that the shoulder and the peak appearing in the swelling behavior of the gel are respectively induced by the criticalities of the binary mixture outside and inside the gel. It also shows that the cloud point temperature lowering of the binary mixture inside the gel is attributed to the effective enhancement of the temperature of the binary mixture inside the gel induced by the presence of the gel polymer.
Prevalence of Novel Myositis Autoantibodies in a Large Cohort of Patients with Interstitial Lung Disease

Connective tissue diseases (CTDs) are an important secondary cause of interstitial lung disease (ILD). If a CTD is suspected, clinicians are recommended to perform autoantibody testing, including for myositis autoantibodies. In this study, the prevalence and clinical associations of novel myositis autoantibodies in ILD are presented. A total of 1194 patients with ILD and 116 healthy subjects were tested for antibodies specific for Ks, Ha, Zoα, and cN1A with a line-blot assay on serum available at the time of diagnosis. Autoantibodies were demonstrated in 63 (5.3%) patients and one (0.9%) healthy control (p = 0.035). Autoantibodies were found more frequently in females (p = 0.042) and patients without a histological and/or radiological usual interstitial pneumonia (UIP; p = 0.010) and a trend towards CTD-ILDs (8.4%) was seen compared with other ILDs (4.9%; p = 0.090). The prevalence of antibodies specific for Ks, Ha, Zoα, and cN1A was, respectively, 1.3%, 2.0%, 1.4%, and 0.9% in ILD. Anti-Ha and Anti-Ks were observed in males with unclassifiable idiopathic interstitial pneumonia (unclassifiable IIP), hypersensitivity pneumonitis (HP), and various CTD-ILDs, whereas anti-cN1A was seen in females with antisynthetase syndrome (ASS), HP, and idiopathic pulmonary fibrosis (IPF). Anti-Zoα was associated with CTD-ILD (OR 2.5; 95%CI 1.11–5.61; p = 0.027). In conclusion, a relatively high prevalence of previously unknown myositis autoantibodies was found in a large cohort of various ILDs. Our results contribute to the awareness that circulating autoantibodies can be found in ILDs with or without established CTD. Whether these antibodies have to be added to the standard set of autoantibodies analysed in conventional myositis blot assays for diagnostic purposes in clinical ILD care requires further study.
How Specialist Aftercare Impacts Long-Term Readmission Risks in Elderly Patients With Metabolic, Cardiac, and Chronic Obstructive Pulmonary Diseases: Cohort Study Using Administrative Data

Background The health state of elderly patients is typically characterized by multiple co-occurring diseases requiring the involvement of several types of health care providers. Objective We aimed to quantify the benefit for multimorbid patients from seeking specialist care in terms of long-term readmission risks. Methods From an administrative database, we identified 225,238 elderly patients with 97 different diagnosis (ICD-10 codes) from hospital stays and contact with 13 medical specialties. For each diagnosis associated with the first hospital stay, we used multiple logistic regression analysis to quantify the sex-specific and age-adjusted long-term all-cause readmission risk (hospitalizations occurring between 3 months and 3 years after the first admission) and how specialist contact impacts these risks. Results Men have a higher readmission risk than women (mean difference over all first diagnoses 1.9%, P<.001), but similar reduction in readmission risk after receiving specialist care. Specialist care can reduce readmission risk by almost 50%. We found the greatest reductions in risk when the first hospital stay was associated with diagnoses corresponding to complex chronic diseases such as acute myocardial infarction (57.6% reduction in readmission risk, SE 7.6% for men [m]; 55.9% reduction, SE 9.8% for women [w]), diabetic and other retinopathies (m: 62.3%, SE 8.0; w: 60.1%, SE 8.4%), chronic obstructive pulmonary disease (m: 63.9%, SE 7.8%; w: 58.1%, SE 7.5%), disorders of lipoprotein metabolism (m: 64.7%, SE 3.7%; w: 63.8%, SE 4.0%), and chronic ischemic heart diseases (m: 63.6%, SE 3.1%; w: 65.4%, SE 3.0%). Conclusions Specialist care can greatly reduce long-term readmission risk for patients with chronic and multimorbid diseases. Further research is needed to identify the specific reasons for these findings and to understand the detected sex-specific differences.
Relationships between Physical and Social Behavioural Changes and the Mental Status of Homebound Residents in Hong Kong during the COVID-19 Pandemic

In Hong Kong, social distancing has been adopted in order to minimise the spread of COVID-19. This study aims to examine the changes in physical health, mental health, and social well-being experienced by local residents who were homebound during the pandemic. An online questionnaire in both Chinese and English versions was completed by 590 eligible participants from 24 April to 13 May 2020. The questionnaire found that individuals aged 18 to 25 years spent more time resting and relaxing but experienced more physical strain. Working status was associated with social contact, with participants working full-time jobs scoring higher in “maintaining social communication via electronic means” and “avoiding social activities outside the home”. Additionally, approximately one third of the participants (29.7%) had moderate to severe depression, and participants aged 18 to 25 were found to have higher scores in PHQ-9. Changes in physical health and social contact were significantly associated with developing depressive symptoms. From the results, it is clear that the COVID-19 pandemic has the potential to exert a negative impact on the mental health status of individuals.
The Current Status of the Alternative Use to Antibiotics in Poultry Production: An African Perspective

Over the years the growth and health of food-producing animals have been enhanced by the use of antibiotics. These have helped reduce on-farm mortalities, lower incidences of diseases and more importantly improve productivity. Generally, the utilization of antibiotics in feed has been reevaluated since bacterial pathogens have established and shared a variety of antibiotic resistance mechanisms that can easily be spread within microbial communities. Multiple countries have introduced bans or severe restrictions on the non-therapeutic use of antibiotics. This has therefore warranted the urgent need for alternatives. Africa is facing its own challenges as it has been reported to be one of the continents with the highest number of foodborne diseases with approximately 91 million related diseases and 137,000 death per annum. Stakeholder and policy direction has been put in place to curb this escalation; however, the problem persists. The use of alternatives has been recommended and some successfully used in other countries as well as Africa, including pro- and prebiotics and phytochemicals. This then leads to the core aim of this review which is to (1) determine the extent to which antimicrobial-resistant pathogens have affected Africa, (2) assess the current measures put in place by Africa to reduces antimicrobial resistance and finally (3) explore the alternative use of antibiotics in poultry production. Improved sanitary conditions and farm biosecurity are important alternatives that could be adopted by farmers instead of depending on antibiotic drugs for disease control and prevention.