Miracle-dz/UniFAR-FTUs huggingface dataset:
Serotyping, MLST, and Core Genome MLST Analysis of Salmonella enterica From Different Sources in China During 2004–2019

Salmonella enterica (S. enterica) is an important foodborne pathogen, causing food poisoning and human infection, and critically threatening food safety and public health. Salmonella typing is essential for bacterial identification, tracing, epidemiological investigation, and monitoring. Serotyping and multilocus sequence typing (MLST) analysis are standard bacterial typing methods despite the low resolution. Core genome MLST (cgMLST) is a high-resolution molecular typing method based on whole genomic sequencing for accurate bacterial tracing. We investigated 250 S. enterica isolates from poultry, livestock, food, and human sources in nine provinces of China from 2004 to 2019 using serotyping, MLST, and cgMLST analysis. All S. enterica isolates were divided into 36 serovars using slide agglutination. The major serovars in order were Enteritidis (31 isolates), Typhimurium (29 isolates), Mbandaka (23 isolates), and Indiana (22 isolates). All strains were assigned into 43 sequence types (STs) by MLST. Among them, ST11 (31 isolates) was the primary ST. Besides this, a novel ST, ST8016, was identified, and it was different from ST40 by position 317 C → T in dnaN. Furthermore, these 250 isolates were grouped into 185 cgMLST sequence types (cgSTs) by cgMLST. The major cgST was cgST235530 (11 isolates), and only three cgSTs contained isolates from human and other sources, indicating a possibility of cross-species infection. Phylogenetic analysis indicated that most of the same serovar strains were putatively homologous except Saintpaul and Derby due to their multilineage characteristics. In addition, serovar I 4,[5],12:i:- and Typhimurium isolates have similar genomic relatedness on the phylogenetic tree. In conclusion, we sorted out the phenotyping and genotyping diversity of S. enterica isolates in China during 2004–2019 and clarified the temporal and spatial distribution characteristics of Salmonella from different hosts in China in the recent 16 years. These results greatly supplement Salmonella strain resources, genetic information, and traceability typing data; facilitate the typing, traceability, identification, and genetic evolution analysis of Salmonella; and therefore, improve the level of analysis, monitoring, and controlling of foodborne microorganisms in China.
Virtual Spatial Channel Number and Index Modulation

This paper proposes a novel precoding-aided and efficient data transmission scheme called virtual spatial channel number and index modulation (VS-CNIM), which conveys extra data by changing both the number and index of active virtual parallel channels of multiple-input multiple-output (MIMO) channels, obtained through the singular value decomposition (SVD) in each time slot. Unlike the conventional virtual spatial modulation (VSM), where extra data bits are transmitted only using index of active virtual parallel channels, the VS-CNIM scheme, depending on incoming information bits, transmits extra bits utilizing both the number and indices of active parallel channels along the bits carried by M -ary constellation symbols. Therefore, VS-CNIM provides significantly superior spectral efficiency (SE) compared to VSM. Considering the influence of imperfect channel estimation, a closed-form upper bound is derived on average bit error probability (ABEP). The asymptotic performance is also analyzed, which gives the coding gain and diversity order and describes error floor under the consideration of perfect and imperfect channel estimation, respectively. Monte Carlo simulations exhibit that the VS-CNIM scheme achieves considerably better error performance and high SE than precoding-aided SM (PSM) and VSM schemes.
A new gene mutation in a family with idiopathic infantile nystagmus

Idiopathic infantile nystagmus (IIN) is an inherited disease, which can occur through a number of different inheritance patterns (autosomal dominant, recessive, or X-linked). The most common of these is X-linked inheritance with incomplete penetrance and variable expressivity, and can also be dominant or recessive. To date, only two mutations have been described: the first, affecting the FPR143 gene, which is associated with ocular albinism type I, and located on chromosome Xp22, and the second, affecting the FRMD7 gene located on chromosome X26-q27. To date, a causative gene on locus Xp11.3p11. 4 has not yet been identified. The most common cause of IIN is due to mutations in the FRMD7 gene, located on chromosome Xq26. We present a case of a new mutation found in three siblings from a family with FRMD7-related infantile nystagmus, whose parents are consanguineously related in the first degree. A complex mutation has occurred in this family, which, to date, has not been previously reported in the scientific literature. The complex mutation consists of the presence of three consecutive 1 bp deletions in exon 12 (c.1248delT; 1299del C; and 1312delT), causing a secondary deletion (c. 1340–2145 + 214del), and resulting in a truncated protein. We also present a 7-year-old patient from a different family, with periodic alternating nystagmus, having no mutation in the FRMD7 gene, which we assume may be an example of non-FRMD7-related IIN. This patient does not have a family history of nystagmus.
The Role of Urinary LH and FSH in the Diagnosis of Pubertal Disorders

Background: Various hormonal parameters used to differentiate between different causes of pubertal disorders are invasive, cumbersome, and has variable sensitivity and specificity. Thus, the use of a noninvasive test like urinary gonadotropin for the diagnosis of pubertal disorders will offer a significant advantage. Objective: To study the role of urinary gonadotropins (uLH, uFSH) for the diagnosis of various pubertal disorders and in the monitoring of Gonadotrophin releasing hormone, Hypothalamic-pituitary-gonadal (GnRHa) therapy in patients with central precocious puberty (CPP). Materials and Methods: We evaluated 35 healthy children and 96 patients with disorders of puberty out of which 31 cases had early puberty and 65 cases had delayed puberty. We used Spearman's correlation coefficient to evaluate the correlation between the serum and urinary gonadotropins. We used Mann–Whitney U test (for 2 groups) and Kruskal–Wallis test (for > 2 groups) to compare the median urinary and serum gonadotropins of different groups. Results: The urinary gonadotropins correlated strongly with serum gonadotropins in both healthy controls and individuals with pubertal disorders. The uLH level of ≥0.76 IU/L had 100% sensitivity and specificity to differentiate CPP from peripheral precocious puberty, whereas uLH level of ≥1.07 IU/L had 100% sensitivity and specificity for differentiating CPP from PT. In patients with delayed puberty, uFSH of ≥20.51 IU/L had 94.7% sensitivity and 91.3% specificity for the diagnosis of Hyper-Hypo cases and uLH level of ≥0.5 IU/L had sensitivity of 96.2% and specificity of 85% to differentiate constitutional delay in growth and puberty from hypogonadotropic-hypogonadism. In CPP patients on GnRHa therapy, the uLH level of ≥0.13 IU/L had 100% sensitivity and 86.7% specificity to identify those who had nonsuppressed serum LH levels. Conclusion: The urinary gonadotropins can be used as a reliable noninvasive test for the diagnosis of various pubertal disorders and also for monitoring of CPP patients on GnRHa therapy.
Cervical deformity patients with baseline hyperlordosis or hyperkyphosis differ in surgical treatment and radiographic outcomes

Introduction: Patients with symptomatic cervical deformity (CD) requiring surgical correction often present with hyperkyphosis (HK), though patients with hyperlordotic curves may require surgery as well. Few studies have investigated differences in CD-corrective surgery with regards to HK and hyperlordosis (HL). Materials and Methods: Operative CD patients (C2-C7 Cobb >10°, cervical lordosis [CL] >10°, cervical sagittal vertical axis [cSVA] >4 cm, chin-brow vertical angle >25°) with baseline (BL) and 1Y radiographic data. Patients were stratified based on BL C2-7 lordosis (CL) angle: those >1 standard deviation (SD) from the mean (−6.96° ±21.47°) were hyperlordotic (>14.51°) or hyperkyphotic (≤28.43°) depending on directionality. Patients within 1 SD were considered the control group. Results: One hundred and two surgical CD pts (61 years, 65%F, 30 kg/m2) with BL and 1Y radiographic data were included. Twenty pts met definitions for HK and 21 pts met definitions for HL. No differences in demographics or disability were noted. HK had higher estimated blood loss (EBL) with anterior approaches than HL but similar EBL with the posterior approach. Op-time did not differ between groups. Control, HL, and HK groups differed in BL TS-CL (36.6° vs. 22.5° vs. 60.7°, P < 0.001) and BL-sagittal vertical axis (SVA) (10.8 vs. 7.0 vs. −47.8 mm, P = 0.001). HL pts had less discectomies, less corpectomies, and similar osteotomy rates to HK. HL had × 3 revisions of HK and controls (28.6 vs. 10.0 vs. 9.2%, respectively, P = 0.046). At 1Y, HL pts had higher cSVA, and trended higher SVA and SS than HK. In terms of BL-upper cervical alignment, HK pts had higher McGregor's-slope (16.1° vs. −3.3°, P = 0.001) and C0-C2 Cobb (43.3° vs. 26.9°, P < 0.001), however postoperative differences in McGregor's slope and C0-C2 were not significant. HK drivers of deformity were primarily C (90%), whereas HL had primary computed tomography (38.1%), upper thoracic (23.8%), and C (14.3%) drivers. Conclusions: Hyperlodotic patients trended higher revision rates with greater radiographic malalignment at 1Y postoperative, perhaps due to undercorrection compared to kyphotic etiologies.
Adipose Tissue Levels of DDT as Risk Factor for Obesity and Type 2 Diabetes Mellitus

Background: Exposure to dichlorodiphenyltrichloroethane (DDT), a potent lipophilic organochlorine pesticide, has long been linked as a risk factor for type 2 diabetes mellitus (T2DM). However, its presence in the adipose tissues of the T2DM subjects has not been explored in the Indian population, where this long-banned pesticide is still in use. The present study was conducted to evaluate the possible association of DDT and its metabolites in obese and non-obese T2DM subjects. Methods: Subjects with normal glucose tolerance (n = 50) and T2DM (n = 50) were divided into equal numbers in obese and non-obese groups. Their plasma glucose levels, HbA1c, and lipid profile were measured. The adipose tissues were collected intraoperatively, and DDT and its metabolites were measured using a gas chromatograph equipped with an electron capture detector. Results: Obese subjects, irrespective of their glycemic status, and T2DM subjects had higher concentrations of DDT. p, p′ DDT was found to increase the odds for diabetes, and o, p′ DDT for central obesity. p, p′ DDD was also strongly correlated with central obesity, glycemic parameters, and triglycerides. Conclusion: The excess deposition of p, p′ DDD, o, p′ DDT, and p, p′ DDT in obese subjects may proceed to T2DM by disrupting triglycerides and glycemic parameters.
Analyses on the distribution and influence of higher-order aberrations both clinically and experimentally among varied refractive errors

PURPOSE: The aim of this work is to determine and compare the distribution and influence of higher-order aberrations (HOAs) both clinically and experimentally between different refractive errors. METHODS: Commercially available Shack–Hartmann aberrometer was employed to measure the HOA clinically in human eyes. Experimentally, HOA was measured in a model eye by simulating various refractive errors by constructing an aberrometer based on the same Shack Hartmann principle. One-way analyses of variance and simple regression were employed to analyze the distribution and influence of HOA among various refractive errors. RESULTS: A total of 100 eyes were clinically measured for aberrations, of which 35, 50, and 15 eyes were emmetropes, myopes, and hyperopes, respectively. Out of the total root mean square (RMS) value, the HOAs found in the human eyes were 23%, 7%, and 26% and in the model eye, it was 20%, 8%, and 10% between emmetropes, myopes, and hyperopes, respectively. The mean higher-order RMS was almost similar between the groups and among various refractive errors. There was no statistical significance between the individual Zernikes except for the coma in both human and model eyes. CONCLUSION: The mean HOA is similar amidst the different refractive errors. The presence of 23% HOA in emmetropes signifies that larger part of the human eye is capable of complying with HOA without compromising the image quality. This work signifies that HOA does not play an important role in image clarity for human eyes with regular refractive surface unlike irregular refractive surfaces.
Framework for Machine Learning of CT and PET Radiomics to Predict Local Failure after Radiotherapy in Locally Advanced Head and Neck Cancers

Context: Cancer Radiomics is an emerging field in medical imaging and refers to the process of converting routine radiological images that are typically qualitatively interpreted to quantifiable descriptions of the tumor phenotypes and when combined with statistical analytics can improve the accuracy of clinical outcome prediction models. However, to understand the radiomic features and their correlation to molecular changes in the tumor, first, there is a need for the development of robust image analysis methods, software tools and statistical prediction models which is often limited in low- and middle-income countries (LMIC). Aims: The aim is to build a framework for machine learning of radiomic features of planning computed tomography (CT) and positron emission tomography (PET) using open source radiomics and data analytics platforms to make it widely accessible to clinical groups. The framework is tested in a small cohort to predict local disease failure following radiation treatment for head-and-neck cancer (HNC). The predictors were also compared with the existing Aerts HNC radiomics signature. Settings and Design: Retrospective analysis of patients with locally advanced HNC between 2017 and 2018 and 31 patients with both pre- and post-radiation CT and evaluation PET were selected. Subjects and Methods: Tumor volumes were delineated on baseline PET using the semi-automatic adaptive-threshold algorithm and propagated to CT; PyRadiomics features (total of 110 under shape/intensity/texture classes) were extracted. Two feature-selection methods were tested for model stability. Models were built based on least absolute shrinkage and selection operator-logistic and Ridge regression of the top pretreatment radiomic features and compared to Aerts' HNC-signature. Average model performance across all internal validation test folds was summarized by the area under the receiver operator curve (ROC). Results: Both feature selection methods selected CT features MCC (GLCM), SumEntropy (GLCM) and Sphericity (Shape) that could predict the binary failure status in the cross-validated group and achieved an AUC >0.7. However, models using Aerts' signature features (Energy, Compactness, GLRLM-GrayLevelNonUniformity and GrayLevelNonUniformity-HLH wavelet) could not achieve a clear separation between outcomes (AUC = 0.51–0.54). Conclusions: Radiomics pipeline included open-source workflows which makes it adoptable in LMIC countries. Additional independent validation of data is crucial for the implementation of radiomic models for clinical risk stratification.
Risk-benefit assessment of major versus minor osteotomies for flexible and rigid cervical deformity correction

Introduction: Osteotomies are commonly performed to correct sagittal malalignment in cervical deformity (CD). However, the risks and benefits of performing a major osteotomy for cervical deformity correction have been understudied. The objective of this retrospective cohort study was to investigate the risks and benefits of performing a major osteotomy for CD correction. Methods: Patients stratified based on major osteotomy (MAJ) or minor (MIN). Independent t-tests and Chi-squared tests were used to assess differences between MAJ and MIN. A sub-analysis compared patients with flexible versus rigid CL. Results: 137 CD patients were included (62 years, 65% F). 19.0% CD patients underwent a MAJ osteotomy. After propensity score matching for cSVA, 52 patients were included. About 19.0% CD patients underwent a MAJ osteotomy. MAJ patients had more minor complications (P = 0.045), despite similar surgical outcomes as MIN. At 3M, MAJ and MIN patients had similar NDI, mJOA, and EQ5D scores, however by 1 year, MAJ patients reached MCID for NDI less than MIN patients (P = 0.003). MAJ patients with rigid deformities had higher rates of complications (79% vs. 29%, P = 0.056) and were less likely to show improvement in NDI at 1 year (0.95 vs. 0.54, P = 0.027). Both groups had similar sagittal realignment at 1 year (all P > 0.05). Conclusions: Cervical deformity patients who underwent a major osteotomy had similar clinical outcomes at 3-months but worse outcomes at 1-year as compared to minor osteotomies, likely due to differences in baseline deformity. Patients with rigid deformities who underwent a major osteotomy had higher complication rates and worse clinical improvement despite similar realignment at 1 year.
Assessment of Uncertainty Depending on Various Conditions in Modulation Transfer Function Calculation Using the Edge Method

In medical X-ray imaging, to perform optimal operations, it is essential for the user to understand whether a required image quality level which depends on a diagnostic task can be achieved with the imaging system used. This study focuses on the effects of noise on the modulation transfer function (MTF) using the edge method, the most widely used to evaluate the task dependence property. The purpose is to verify the uncertainty of the MTF value at each spatial frequency and examine the conditions under which the accuracy is ensured. By using a Monte Carlo simulation, edge images with various contrast-to-noise ratio (CNR) are acquired. MTFs are then calculated with different edge spread function (ESF) lengths. The uncertainties for each spatial frequency are estimated based on the independent MTF calculations obtained from the five edge data. The uncertainty of the MTF is inversely proportional to the CNR. In the frequency range up to the Nyquist frequency, the uncertainty in five calculations is <0.01 when the CNR is more than 60. In addition, it is observed that the uncertainty increases as the ESF length increases. This relationship depends on the frequency range, but it is proportional to the 0.3–0.5 power of the ESF length. The results in which the uncertainty is most likely to be large in the MTF calculation are clearly shown. Therefore, it is expected to provide an important barometer and useful insights for a proper image quality measurement.
Determining Reasons Affecting the Late Treatment of Congenital Talipes Equinovarus: A Qualitative Study

BACKGROUND: Neglected congenital talipes equinovarus (CTEV) is a serious problem commonly found in developing countries. This deformity has fatal impacts, including disabilities and educational limitations. Moreover, cases of neglected CTEV are still frequent in Indonesia as one of the developing countries. Thus, this study aims to investigate the reasons behind the late treatment of CTEV. METHODS: This is a qualitative study conducted throughout September 2019. The subjects are six parents of patients with neglected CTEV who are currently being treated in our hospital. The study was conducted by performing an in-depth interview with the patient’s parents to analyze why they delay checking their child to an orthopaedic surgeon. The results were then grouped into themes. RESULTS: The reasons for the delay were multifactorial. Four subjects had more than one reason why they delayed checking their child to an orthopaedic surgeon. The reason for the delay were socioeconomic factors (3 subjects), medical-related problems (3 subjects), intentionally delayed or refused to seek medical care (2 subjects), and misinformation from the previous physician (3 subjects). CONCLUSIONS: The reasons for the late treatment of CTEV were socioeconomic factors, medical-related problems, intentional factors, and misinformation.
Role of Credit Risk in Performance difference between A and B Class Banks in Nepal

This paper explains the performance differences between A and B class financial institutions arising from credit risk. The dynamic panel data from 2008 to 2019 has been considered from all 28 commercial banks and 11 national level development banks for analysis. Arellano Bond method has been performed to control the unobserved heterogeneity and to reduce biasness in the parameter estimation as they have both cross sectional and time dimensions. The results have shown clear differences in credit risk status between A class and B class bank with all the parameters except for Return on Assets (ROA). The results show that the A class commercial banks are less vulnerable than the B class bank as measured by Standard deviation of ROA ( standard deviation of return on equity (SDROE) both, yet offer substantially higher ROE and fairly higher NIM. Findings suggest that the past performance BFIs, regardless their classes, are capable enough to predict their future performance as all lag variables are significant. Development banks are advised to focus on maintaining appropriate credit to deposit ratio (CDR) as it has been affecting most of the performance indicators whereas, commercial banks are advised to monitor their loan loss provision to total loans and advances (LLPTLA) for better performance. The control variables have been found to have negligible effect on performance of banks yet higher inflation deteriorates the performance even at a small amount. Further, contradictory findings on influence of real gross domestic product (GDP) growth with the performance demands a need of further research. To recapitulate, the credit risk plays a vital role in performance of banks in Nepal and A class banks safer with returns.
Intangibles, Concentration, and the Labor Share∗

Over the past three decades, the U.S. business sector has been characterized by increasing concentration and decreasing measured labor share. Over the same period, investment in BEA-measured intangible capital, mainly software and R&D, has grown rapidly as a share of total business income. This paper develops a quantitative general equilibrium model of firm dynamics and shows that intangibles play a key role in understanding the trends in measured labor share and concentration jointly, taking both the intangible-related technical change and measurement issue of labor share into consideration. The model is consistent with important aspects of firm behavior at the micro level. An intangible-investment-specific technical change (IISTC) shifts the distribution of firms toward large, intangible-intensive firms with low labor shares. When the IISTC is calibrated to match the observed decline in the relative price of intangible investment goods, the model can account for a significant part of the observed rise in concentration and the observed decline in the measured labor share jointly.