Miracle-dz/UniFAR-FTUs huggingface dataset:
Optical second‐harmonic scattering in rat‐tail tendon

The angular dependence of optical second‐harmonic generation by native, wet, rat‐tail tendon is found to display a sharp, intense, forward peak superimposed on a broad background. The sharp peak is shown to imply long‐range polar order, while the broad background corresponds to that predicted for the random “up”/“down” array of collagen fibrils seen with the electron microscope. The degree of polar order is determined, and the dependence of the fibril diameter distribution on age and state of hydration is measured. The coherence length of tendon for harmonic generation and the absolute magnitude of the nonlinear susceptibility of the collagen fibril are also determined. The biological significance of these various findings is discussed.
Random correlation matrices

Given a bijective vectorial Boolean function Z~ -1Z~, define the correlation matrix P as an N x N matrix, N = 2n 1, whose entries are given as the squares of the correlation coefficients between nonzero linear combinations of the component Boolean functions of F and nonzero linear Boolean functions of the same n variables. Let A denote the number of nonzero entries in P. When F is chosen uniformly at random, the expected value and variance of A are determined. As a consequence, it is shown that for any 'YN = o(N), the fraction of all F such that A::S; N'YN is o(N-1). Similar results are also obtained for partially linear F. When F is such that (1 cn)n component functions of F are necessarily linear, where cnn -100 as n -100, it is derived that for any 'YN = o(N), the fraction of all F such that A ::s; N'YN is O(Ncn -2).
Monitoring daily milk yields with a recursive test day repeatability model (Kalman filter).

Mixed model methodology and recursive estimation techniques (Kalman filter) were combined to detect significant changes in the performance level of both individual cows and an entire herd. Yields were predicted for the next time of recording using all data available up to that time. Predicted yields were compared with actual measurements. If the error of prediction, or innovation, exceeded +/- 2 times its standard deviation, the observation was considered to be significantly different from the former yield level. The data comprised 30,199 records for 135 cows and 366 d. Effects fitted in the model were test day, breed, and lactation class as fixed effects and cow within lactation number as a random effect. A lactation curve was fitted within lactation class. Of the observed milk yields, 9.2% deviated significantly from the expected value in a negative direction. None of the innovation of the fixed-day effect exceeded the threshold of two standard deviations. Compared with the results of rolling average, which were calculated as the average of a 10-d period, over 20% of the observations of the daily milk yield were classified differently by the two methods. The mixed-model method for recursive estimation takes better account of environmental and lactational effects influencing daily milk yields as the rolling average. The mixed-model recursive estimation method was applicable for the detection of suspicious (i.e., outside a specified prediction interval) observations of individual cows at the time of the actual recording.
Deep Learning in Mammography: Diagnostic Accuracy of a Multipurpose Image Analysis Software in the Detection of Breast Cancer

Objectives The aim of this study was to evaluate the diagnostic accuracy of a multipurpose image analysis software based on deep learning with artificial neural networks for the detection of breast cancer in an independent, dual-center mammography data set. Materials and Methods In this retrospective, Health Insurance Portability and Accountability Act-compliant study, all patients undergoing mammography in 2012 at our institution were reviewed (n = 3228). All of their prior and follow-up mammographies from a time span of 7 years (2008–2015) were considered as a reference for clinical diagnosis. After applying exclusion criteria (missing reference standard, prior procedures or therapies), patients with the first diagnosis of a malignoma or borderline lesion were selected (n = 143). Histology or clinical long-term follow-up served as reference standard. In a first step, a breast density-and age-matched control cohort was selected (n = 143) from the remaining patients with more than 2 years follow-up (n = 1003). The neural network was trained with this data set. From the publicly available Breast Cancer Digital Repository data set, patients with cancer and a matched control cohort were selected (n = 35 × 2). The performance of the trained neural network was also tested with this external data set. Three radiologists (3, 5, and 10 years of experience) evaluated the test data set. In a second step, the neural network was trained with all cases from January to September and tested with cases from October to December 2012 (screening-like cohort). The radiologists also evaluated this second test data set. The areas under the receiver operating characteristic curve between readers and the neural network were compared. A Bonferroni-corrected P value of less than 0.016 was considered statistically significant. Results Mean age of patients with lesion was 59.6 years (range, 35–88 years) and in controls, 59.1 years (35–83 years). Breast density distribution (A/B/C/D) was 21/59/42/21 and 22/60/41/20, respectively. Histologic diagnoses were invasive ductal carcinoma in 90, ductal in situ carcinoma in 13, invasive lobular carcinoma in 13, mucinous carcinoma in 3, and borderline lesion in 12 patients. In the first step, the area under the receiver operating characteristic curve of the trained neural network was 0.81 and comparable on the test cases 0.79 (P = 0.63). One of the radiologists showed almost equal performance (0.83, P = 0.17), whereas 2 were significantly better (0.91 and 0.94, P < 0.016). In the second step, performance of the neural network (0.82) was not significantly different from the human performance (0.77–0.87, P > 0.016); however, radiologists were consistently less sensitive and more specific than the neural network. Conclusions Current state-of-the-art artificial neural networks for general image analysis are able to detect cancer in mammographies with similar accuracy to radiologists, even in a screening-like cohort with low breast cancer prevalence.
Exome Sequencing in an Admixed Isolated Population Indicates NFXL1 Variants Confer a Risk for Specific Language Impairment

Children affected by Specific Language Impairment (SLI) fail to acquire age appropriate language skills despite adequate intelligence and opportunity. SLI is highly heritable, but the understanding of underlying genetic mechanisms has proved challenging. In this study, we use molecular genetic techniques to investigate an admixed isolated founder population from the Robinson Crusoe Island (Chile), who are affected by a high incidence of SLI, increasing the power to discover contributory genetic factors. We utilize exome sequencing in selected individuals from this population to identify eight coding variants that are of putative significance. We then apply association analyses across the wider population to highlight a single rare coding variant (rs144169475, Minor Allele Frequency of 4.1% in admixed South American populations) in the NFXL1 gene that confers a nonsynonymous change (N150K) and is significantly associated with language impairment in the Robinson Crusoe population (p = 2.04 × 10–4, 8 variants tested). Subsequent sequencing of NFXL1 in 117 UK SLI cases identified four individuals with heterozygous variants predicted to be of functional consequence. We conclude that coding variants within NFXL1 confer an increased risk of SLI within a complex genetic model.
COMPUTED TOMOGRAPHY UROGRAPHY FOR DIAGNOSING BLADDER CANCER

Thus regrettably, the conclusions of this paper are inappropriate and quite misleading. Probably, the most important lesson of this report is that fine-needle aspiration is not feasible in diagnosing CIS. Finally, we reemphasize that according to current guidelines, a thorough morphological examination of testicular biopsy specimens is indispensable in diagnosing CIS (TIN). Intact seminiferous tubules are essential for an accurate morphological assessment of cells under suspicion of representing CIS. Immunohistochemical staining of PLAP or other immunohistochemical markers might be used as an adjunct [4].
Long-read sequencing improves assembly of Trichinella genomes 10-fold, revealing substantial synteny between lineages diverged over 7 million years

SUMMARY Genome assemblies can form the basis of comparative analyses fostering insight into the evolutionary genetics of a parasite's pathogenicity, host–pathogen interactions, environmental constraints and invasion biology; however, the length and complexity of many parasite genomes has hampered the development of well-resolved assemblies. In order to improve Trichinella genome assemblies, the genome of the sylvatic encapsulated species Trichinella murrelli was sequenced using third-generation, long-read technology and, using syntenic comparisons, scaffolded to a reference genome assembly of Trichinella spiralis, markedly improving both. A high-quality draft assembly for T. murrelli was achieved that totalled 63·2 Mbp, half of which was condensed into 26 contigs each longer than 571 000 bp. When compared with previous assemblies for parasites in the genus, ours required 10-fold fewer contigs, which were five times longer, on average. Better assembly across repetitive regions also enabled resolution of 8 Mbp of previously indeterminate sequence. Furthermore, syntenic comparisons identified widespread scaffold misassemblies in the T. spiralis reference genome. The two new assemblies, organized for the first time into three chromosomal scaffolds, will be valuable resources for future studies linking phenotypic traits within each species to their underlying genetic bases.
The polymorphism of the ATP-binding cassette transporter 1 gene modulates Alzheimer disease risk in Chinese Han ethnic population.

BACKGROUND Recent studies highlight a potential role of cholesterol metabolic disturbance in the pathophysiology of Alzheimer disease (AD). The adenosine triphosphate (ATP)-binding cassette transporter 1 (ABCA1) gene resides within proximity of linkage peaks on chromosome 9q influence AD and plays a key role in cellular cholesterol efflux in the brain. METHODS We studied the role of R219K and V825I polymorphisms of ABCA1 in modulating the risk of AD in 321 AD patients and 349 comparisons of Chinese Han. Genotyping of R219K and V825I were performed by PCR-restriction fragment length polymorphism analysis. RESULTS The genotype distribution of R219K was different with more RK in total AD group (χ(2) = 8.705, df = 2, p = 0.013), late-onset AD (LOAD) group (χ(2) = 10.636, df = 2, p = 0.005), APOE non-ε4ε4 group (χ(2) = 9.900, df = 2, p = 0.007), and female AD group (χ(2) = 8.369, df = 2, p = 0.015). Logistic regression manifested the risk of AD increased in RK carriers in total AD group (Wald = 6.102, df = 1, p = 0.014, odds ratio [OR]: 1.546, 95% confidence interval [95% CI]: 1.094-2.185), LOAD group (Wald = 7.746, df = 1, p = 0.005, OR: 1.921, 95% CI: 1.213-3.041), and APOE non-ε4ε4 group (Wald = 6.399, df = 1, p = 0.011, OR: 1.586, 95% CI: 1.109-2.266). K allele (RK + KK) also increased the risk of AD compared with RR allele in LOAD group (Wald = 4.750, df = 1, p = 0.029, OR: 1.619, 95% CI: 1.050-2.497). However, no discrepancy was found in V825I. In R219K, age at onset (AAO) was significantly lower by 4.9 years on average in patients of KK genotype than those of RK in APOE ε4 carrying group and higher by 5.5 years in patients of KK genotype than those of RR in APOE ε4 noncarrying group. In V825I, AAO was diseased by 4.3 years in II genotype compared with VV genotype in APOE ε4 noncarrying group and 3.4 years in APOE ε4ε4 noncarrying group. CONCLUSION The results indicated that the RK genotype or K allele (RK + KK) of R219K may relate to the development of AD in the east of China.
MAIZE SEED STORAGE MYCOFLORA IN PAKISTAN AND ITS CHEMICAL CONTROL

Eleven seed-borne fungal species were recorded in the 18 maize seed samples collected from 6 maize growing districts of Punjab and Khyber-Pakhtoonkhwa, Pakistan. Aspergillus flavus, A. niger and Fusarium moniliforme were the most prevalent species with the incidence range up to 94, 62 & 43%, respectively. Maximum number of fungal species i.e., 10 was observed from Okara, Sahiwal and Nowshehra, 9 from Mansehra, whereas 8 were recorded from Mardan and Pakpattan samples. A comparative study was designed to evaluate eight fungicides to control maize seed mycoflora at the rate of 2.0, 2.5, 3.0 and 3.5 g kg. Benlate followed by Thiophanate Methyl and Thiram provided the maximum fungal control at the dose of 3 and 3.5 g kg. Maximum germination percentage was attained in case of seed dressing with Benlate followed by Thiram and Thiophanate methyl at the rate of 3g kg, which revealed Benlate to be a broad spectrum seed dressing fungicide with no adverse effect on germination.
Effect of Fruit Size and Orientation on Mechanical Properties of Gmelina Fruit (Gmelina arborea) Under Quasi-Static Loading

47 www.erpublication. org  Abstract— The knowledge of mechanical properties biomaterials is essential for the proper design of harvesting and processing machineries. In this study, seven mechanical parameters (failure force, failure energy, maximum compressive force, rupture force, rupture energy, maximum strain and relative deformation at rupture) of gmelina fruit was measured at three different fruit sizes (small, medium and large) and in two different fruit orientations (axial and Longitudinal), at a loading speed of 20 mm/min. The results obtained statistically showed that fruit size significantly (P < 0.05) affected the failure force, maximum compressive force, rupture force, rupture energy, maximum compressive strain, and relative deformation of the gmelina fruit; while it does not significantly (P < 0.05) affected the failure energy. Failure force was 51.01, 67.16 and 86.28; maximum compressive force was 156.47, 204.99, 263.65; Rupture force was 146.82, 185.25 and 238.57 N; Failure energy was 0.186, 0.229 and 0 . 293 Nm; Rupture Energy was 0.899, 1.149, and 1475 Nm; maximum strain was 45.25, 61.69 and 79.43%; and relative deformation at rupture was 10.16, 13.13 and 16.89 mm respectively for the small, medium and large gemila fruit. The fruit loading orientation significantly (P < 0.05) influenced all the seven mechanical parameters tested apart from the failure force. Also, the result show that gmelina fruit was more flexible in the Longitudinal loading orientation, in all the seven mechanical parameters studied, as the and energy required to initiate failure and rupture of the fruit under axial loading direction was lower than under Longitudinal loading. In respite to the fruit size, the all the seven parameters studied increased progressively from the small size through the medium to the large fruit.
Diet and Helicobacter pylori infection

Helicobacter pylori infection has accompanied man for thousands of years. In some infected patients, a complex and dynamic pathogen-host reaction triggers pathogenic pathways resulting in development, inter alia, of atrophic gastritis, peptic ulcer disease (both gastric and duodenal), gastric adenocarcinoma, and MALT lymphoma. Large-scale eradication therapy is associated with a rapid increase in antibiotic resistance, gut flora composition disturbances, and increased risk of development, inter alia, of paediatric infectious diarrhoeas, atopic diseases, and oesophageal adenocarcinoma. Our diet contains many substances with potent antibacterial activity against H. pylori. Dietary interventions enable a decrease in H. pylori colonisation and result in a decrease in gastritis prevalence, thus potentially lowering the risk of gastric adenocarcinoma development.
Azithromycin and the Treatment of Lymphocytic Airway Inflammation After Lung Transplantation

Lymphocytic airway inflammation is a major risk factor for chronic lung allograft dysfunction, for which there is no established treatment. We investigated whether azithromycin could control lymphocytic airway inflammation and improve allograft function. Fifteen lung transplant recipients demonstrating acute allograft dysfunction due to isolated lymphocytic airway inflammation were prospectively treated with azithromycin for at least 6 months (NCT01109160). Spirometry (FVC, FEV1, FEF25–75, Tiffeneau index) and FeNO were assessed before and up to 12 months after initiation of azithromycin. Radiologic features, local inflammation assessed on airway biopsy (rejection score, IL‐17+ cells/mm2 lamina propria) and broncho‐alveolar lavage fluid (total and differential cell counts, chemokine and cytokine levels); as well as systemic C‐reactive protein levels were compared between baseline and after 3 months of treatment. Airflow improved and FeNO decreased to baseline levels after 1 month of azithromycin and were sustained thereafter. After 3 months of treatment, radiologic abnormalities, submucosal cellular inflammation, lavage protein levels of IL‐1β, IL‐8/CXCL‐8, IP‐10/CXCL‐10, RANTES/CCL5, MIP1‐α/CCL3, MIP‐1β/CCL4, Eotaxin, PDGF‐BB, total cell count, neutrophils and eosinophils, as well as plasma C‐reactive protein levels all significantly decreased compared to baseline (p < 0.05). Administration of azithromycin was associated with suppression of posttransplant lymphocytic airway inflammation and clinical improvement in lung allograft function.
Double Biocatalysis Signal Amplification Glucose Biosensor Based on Porous Graphene

Controllable preparation of nanopores to promote the performance of electrochemical biosensing interfaces has become one of the researching frontiers in biosensing. A double biocatalysis signal amplification of glucose biosensor for the study of electrochemical behaviors of glucose oxidase (GOx) was proposed by using horseradish peroxidase biosynthesized porous graphene (PGR) as the platform for the biocatalytic deposition of gold nanoparticles (AuNPs). The biosensor showed a linear range from 0.25 to 27.5 μM with a detection limit of 0.05 μM (S/N = 3) towards glucose. Furthermore, the proposed AuNPs/GOx–PGR modified glassy carbon electrode (AuNPs/GOx–PGR/GCE) achieved direct electron transfer of GOx.
Reducing ammonia emissions and volatile fatty acids in poultry litter with liquid aluminum chloride

This study was a pen trial in which the effects of adding different rates of liquid aluminum chloride (AlCl3) on litter pH, total volatile fatty acids (VFAs), and ammonia (NH3) fluxes was evaluated. Liquid AlCl3 treatments used in this study were sprayed on the rice hull surface at rates of 100 g, 200 g, and 300 g liquid AlCl3/kg rice hulls; untreated rice hulls served as controls. Litter pH, total VFAs, and NH3 fluxes were all lowered (P< 0.05) by all of the liquid AlCl3 treatments compared with controls during certain times of the 5 week study. However, there were no significant differences among treatments on litter pH at the end of the study (from 3 to 5 weeks) or NH3 fluxes at beginning of the study (0 to 3 weeks). Total VFAs were reduced 16 %, 29 %, and 53 % by 100 g liquid AlCl3/kg rice hulls, 200 g liquid AlCl3/kg rice hulls, and 300 g liquid AlCl3/kg rice hulls, respectively. Liquid AlCl3additions reduced NH3 fluxes by 35 %, 57 % and 67 %, respectively, at the low, medium and high rates. In summary, these results indicate that adding liquid aluminum chloride to rice hulls would be a useful tool in reducing the negative environmental impact of poultry litter. It should be noted that the decreased VFA production and NH3 volatilization was chiefly associated with reduction in litter pH.
Flow cytometric isolation and clonal identification of self‐renewing bipotent hepatic progenitor cells in adult mouse liver

The adult liver progenitor cells appear in response to several types of pathological liver injury, especially when hepatocyte replication is blocked. These cells are histologically identified as cells that express cholangiocyte markers and proliferate in the portal area of the hepatic lobule. Although these cells play an important role in liver regeneration, the precise characterization that determines these cells as self‐renewing bipotent primitive hepatic cells remains to be shown. Here we attempted to isolate cells that express a cholangiocyte marker from the adult mouse liver and perform single cell‐based analysis to examine precisely bilineage differentiation potential and self‐renewing capability of these cells. Based on the results of microarray analysis and immunohistochemistry, we used an antibody against CD133 and isolate CD133+ cells via flow cytometry. We then cultured and propagated isolated cells in a single cell culture condition and examined their potential for proliferation and differentiation in vitro and in vivo. Isolated cells that could form large colonies (LCs) in culture gave rise to both hepatocytes and cholangiocytes as descendants, while maintaining undifferentiated cells by self‐renewing cell divisions. The clonogenic progeny of an LC‐forming cell is capable of reconstituting hepatic tissues in vivo by differentiating into fully functional hepatocytes. Moreover, the deletion of p53 in isolated LC‐forming cells resulted in the formation of tumors with some characteristics of hepatocellular carcinoma and cholangiocarcinoma upon subcutaneous injection into immunodeficient mutant mice. These data provide evidence for the stem cell‐like capacity of isolated and clonally cultured CD133+ LC‐forming cells. Conclusion: Our method for prospectively isolating hepatic progenitor cells from the adult mouse liver will facilitate study of their roles in liver regeneration and carcinogenesis. (HEPATOLOGY 2008;48:1964‐1978.)
Malignant gastrointestinal melanoma with an unknown primary

Malignant melanoma is rare in India; melanoma presenting as a metastatic disease with an unknown primary, involving the gastrointestinal tract without involving lymph nodes is extremely uncommon. We report a case of a 28-year-old male with a malignant melanoma metastasizing to stomach and liver with an unknown primary. Relevant literature is being reviewed.
Progressive mixture rules are deviation suboptimal

We consider the learning task consisting in predicting as well as the best function in a finite reference set G up to the smallest possible additive term. If R(g) denotes the generalization error of a prediction function g, under reasonable assumptions on the loss function (typically satisfied by the least square loss when the output is bounded), it is known that the progressive mixture rule ĝ satisfies ER(ĝ) ≤ ming∈G R(g) + Cst log|G|/n, (1) where n denotes the size of the training set, and E denotes the expectation w.r. t. the training set distribution. This work shows that, surprisingly, for appropriate reference sets G, the deviation convergence rate of the progressive mixture rule is no better than Cst/√n: it fails to achieve the expected Cst/n. We also provide an algorithm which does not suffer from this drawback, and which is optimal in both deviation and expectation convergence rates.