Miracle-dz/UniFAR-FTUs huggingface dataset:
SPSS for introductory statistics : use and interpretation

1. Variables, Research Problems and Questions. 2. Data Coding, Entry, and Checking. 3. Measurement and Descriptive Statistics. 4. Understanding Your Data and Checking Assumptions. 5. Data File Management and Descriptive Statistics. 6. Selecting and Interpreting Inferential Statistics. 7. Cross-Tabulation, Chi-Square, and Nonparametric Measures of Association. 8. Correlation and Regression. 9. Comparing Two Groups with t Tests and Similar Nonparametric Tests. 10. Analysis of Variance (ANOVA). Appendix A: Getting Started and Other Useful SPSS Procedures. Appendix B: Writing Research Problems and Questions. Appendix C: Making Tables and Figures. Appendix D: Answers to Odd Numbered Interpretation Questions.
Plasma and stool metabolomic biomarkers of non-alcoholic fatty liver disease in Argentina

Background and Aims: Non-invasive biomarkers are urgently needed to identify patients with non-alcoholic fatty liver disease (NAFLD) especially those at risk of disease progression. This is particularly true in high prevalence areas such as Latin America. The gut microbiome and intestinal permeability may play a role in the risk of developing NAFLD and NASH, but the mechanism by which microbiota composition disruption (or dysbiosis) may affect NAFLD progression is still unknown. Targeted metabolomics is a powerful technology for discovering new associations between gut microbiome-derived metabolites and disease. Thus, we aimed to identify potential metabolomic biomarkers related to the NAFLD stage in Argentina, and to assess their relationship with clinical and host genetic factors. Materials and methods: Adult healthy volunteers (HV) and biopsy-proven simple steatosis (SS) or non-alcoholic steatohepatitis (NASH) patients were recruited. Demographic, clinical and food frequency consumption data, as well as plasma and stool samples were collected. SNP rs738409 (PNPLA3 gene) was determined in all volunteers. HPLC and flow injection analysis with MS/MS in tandem was applied for metabolomic studies using the MxP Quant 500 Kit (Biocrates Life Sciences AG, Austria). Significantly different metabolites among groups were identified with MetaboAnalyst v4.0. Bivariate and multivariate analyses were used to identify variables that were independently related to NAFLD stage. Forward stepwise logistic regression models were constructed to design the best feature combination that could distinguish between study groups. Receiver Operating Characteristic (ROC) curves were used to evaluate models' accuracy. Results: A total of 53 volunteers were recruited: 19 HV, 12 SS and 22 NASH. Diet was similar between groups. The concentration of 33 out of 424 detected metabolites (25 in plasma and 8 in stool) was significantly different among study groups. Levels of triglycerides (TG) were higher among NAFLD patients, whereas levels of phosphatidylcholines (PC) and lysoPC were depleted relative to HV. The PNPLA3 risk genotype for NAFLD and NASH (GG) was related to higher plasma levels of eicosenoic acid FA(20:1) (p<0.001). Plasma metabolites showed a higher accuracy for diagnosis of NAFLD and NASH when compared to stool metabolites. Body mass index (BMI) and plasma levels of PC aa C24:0, FA(20:1) and TG(16:1_34:1) showed high accuracy for diagnosis of NAFLD; whereas the best AUROC for discriminating NASH from SS was that of plasma levels of PC aa C24:0 and PC ae C40:1. Conclusion: A panel of plasma and stool biomarkers could distinguish between NAFLD and NASH in a cohort of patients from Argentina. Plasma biomarkers may be diagnostic in these patients and could be used to assess disease progression. Further validation studies including a larger number of patients are needed.
A Generalized Grouping Scheme in Coded Caching

Coded caching, which could significantly reduce the maximum amount of transmission rate during the peak traffic times in wireless network, has been widely studied recently. Apart from the transmission rate, sub-packetization $F$ reflecting the implementation complexity, is also concerned in coded caching. The grouping method proposed by Shanmugam et al. is well-known and widely used to reduce the sub-packetization level of the coded caching problem. In this paper, we propose a concatenating construction method for coded caching schemes, which generalizes the grouping method. Moreover, we demonstrate the advantage of our method in reducing the transmission rate over the grouping method. In particular, some new explicit schemes are obtained from previously known schemes. From one of these schemes, we can derive all the results by Tang and Ramamoorthy as special cases. Furthermore, the analysis and comparison of these new schemes are also performed.
Sexual Dimorphism in Gynodioecious Sidalcea hirtipes (Malvaceae). II. Floral Traits

A morphometric study of 14 floral traits in females and hermaphrodites of Sidalcea hirtipes was conducted to test the hypothesis that the sexual dimorphism in corolla size can be explained entirely by size of the androecium (vestigial in females), as predicted by the corolla‐androecium developmental correlation hypothesis. Overall, corolla, sepal, and stamen sizes were highly intercorrelated, while style length was largely orthogonal to these variables. Hermaphrodites significantly exceeded females in size of most corolla dimensions. However, ANCOVA revealed that the sex difference in corolla size can be attributed solely to the difference in stamen length. These results are consistent with the hypothesis that the androecium is an important regulatory organ for floral development and that one pleiotropic effect of male sterility in S. hirtipes has been a reduction in corolla size. However, length of style and sepals did not conform to this pattern, indicating that these traits are more independent of androecium function than most dimensions of corolla size.
An isolate morphologically and phylogenetically distinct from Botrytis cinerea obtained from withered grapes possibly represents a new species of Botrytis

Grapes kept after harvest for withering in drying fruit rooms (fruttaio) are highly susceptible to Botrytis cinerea infection. A taxonomically undefined isolate (B83) was identified during a survey of B. cinerea populations in these specific environments. This isolate yielded negative results in B. cinerea-specific PCRs and displayed a different colony morphology on potato dextrose agar. Based on this data, the isolate underwent a taxonomic investigation. Sequencing of the ITS–5·8S–ITS2 region indicated that the isolate belongs to the Botrytis genus. IGS-RFLP analysis revealed that Botrytis sp. B83 was a different haplotype from genotypes of indigenous B. cinerea strains. Comparative sequence analysis of three housekeeping genes, G3PDH, HSP60 and RPB2, showed that the isolate constitutes a taxon related to Botrytis aclada, distant from B. cinerea. A phylogenetic tree built with NEP genes was in agreement with the combined tree built with G3PDH, HSP60 and RPB2 sequences. Botrytis sp. B83 is morphologically similar to B. aclada. Conversely, its host range indicates that it is polyphagous like B. cinerea, despite its lower virulence. This study provides evidence for the existence of a new species of Botrytis. Nevertheless, the description of only a single isolate and the need for further information on genetic divergence, reproductive isolation and host preference, prevent the classification and formal description of a new taxon.
An investigation into the effect of skeletal muscle metabolic function & cardio-respiratory fitness on exercise capacity in the presence and absence of disease

It is uncommon for cardio-respiratory fitness and skeletal muscle metabolic function to be assessed independently within an exercise test. Exercise capacity may require adaptation of one or other of these systems to a greater or lesser extent and the presence of disease may affect them to different extents. The physiological mechanisms underpinning the decline in exercise tolerance with age/disease and the benefits of exercise-training as a preventative therapy for some diseases are not fully understood. In this thesis functional capacity was assessed in terms of oxidative capacity. Near-Infrared Spectroscopy (NIRS) measures microvascular changes in oxygenated and deoxygenated haemoglobin and can be used to estimate oxidative capacity in skeletal muscle when combined with arterial occlusions. Oxidative capacity of skeletal muscle was determined as part of 3 studies; (1) in a group of older adults (>65 years old) with or without type 2 diabetes (T2D), (2) in a tri-ethnic group of older adults from the same cohort with the objective of determining ethnic difference in oxidative capacity independently of T2D and (3) in a group of young adults before and after a period of endurance training in preparation for their first marathon. NIRS measurements of muscle oxidative capacity revealed poorer function in older adults with diabetes (57.5±6.8 versus 38.7±2.6 s, p=0.02) and poorer oxidative capacity in South Asian older adults independently of T2D (difference (95%CI): 10.1 (2.3, 17.9) s, p=0.011). In young healthy men and women, skeletal muscle oxygen consumption post-exercise increased with endurance training (p<0.01) despite no improvement in cardio-pulmonary peakVO2 (p=0.81). Faster marathon completion time correlated with cardio-pulmonary peakVO2 (rpartial=-0.55, p< 0.01) but not oxidative capacity. Skeletal muscle oxidative capacity can be measured in old and young adults using NIRS combined with arterial occlusion performed immediately following exercise testing. People with T2D have poorer oxidative capacity compared to people without and South Asians have poorer oxidative capacity compared to Europeans which African Caribbean’s and Europeans had similar skeletal muscle oxidative capacity. Skeletal muscle metabolic adaptions occur following 6 months of endurance training. Although the cardio-pulmonary system is limiting for running performance, skeletal muscle changes can be detected despite no significant improvement in cardio-pulmonary function.
ESTIMATION OF ENDOCRANIAL VOLUME THROUGH THE USE OF EXTERNAL SKULL MEASURES IN THE CARNIVORA (MAMMALIA)

Abstract Allometric relationships of brain and body size in the mammalian order Carnivora have been studied with respect to the pattern and timing of brain-size evolution and aspects of life history, adaptation, and ecology. Analyses of character evolution are aided by inclusion of relevant fossil data; however, endocranial volumes for fossil taxa have been limited to a few cases of extraordinary preservation, reducing the power of analyses. A method for estimating the volume of the brain from external braincase measurements of extant carnivorans is developed here. Multiple linear regression, combined with Akaike information criterion–based model averaging, was employed to predict endocranial volume from 3 external skull measures for 825 museum specimens of 126 extant terrestrial taxa spanning the Carnivora. The AIC-averaged model accurately predicted endocranial volumes for carnivoran taxa (R2 = 0.983), and the results were robust to potential sampling problems. Moreover, the model did not reflect phylogenetic autocorrelation, nor did it represent an induced correlation due to a general body-size scaling. Rather, the averaged model was an accurate predictor of brain volume that should be easily extendable to the carnivoran fossil record, and additionally can be generalized to construct similar models for a broad range of mammalian clades. This in turn will allow comparative studies within and among distantly related mammalian lineages and reconstructions of brain volumes for a diverse array of fossil taxa.
Indirect Diode Laser in the Treatment of Retinopathy of Prematurity

Retinopathy of prematurity (ROP) is a largely preventable cause of visual impairment in children. The golden standard of treatment in ROP is the laser photocoagulation of the nonvascularized retina. The most vulnerable period when ROP is at high risk of rapid progression is comprised between 34 and 35 weeks postconceptional age (PCA) and 36–37 weeks PCA.We carried out a retrospective study in which we included all the ROP cases treated by indirect diode laser photocoagulation between January 1, 2006, and December 31, 2017, totalizing 110 premature infants of which, 60 were males (54.54%) and 50, females (45.45%). Mean gestational age (GA) was 28.30 weeks and mean birth weight (BW) was 1121 grams in our series. Of the 110 preterm infants, 74 were the result of single pregnancies (67.27%) and 36 of multiple pregnancies (32.72%). At the moment of treatment, the mean postnatal age (PNA) was 8.38 weeks and the mean PCA, 37.02 weeks. ROP regressed after laser treatment in 185 eyes (88.09%). Statistical tests proved that regression rate was significantly worse in aggressive posterior ROP as compared with stage 3 zone 2 and stage 3 zone 1 ROP (odds ratio = 13.53, relative risk = 7.79, P < .001).
Detection of new Crimean-Congo hemorrhagic fever virus genotypes in ticks feeding on deer and wild boar, Spain.

Crimean-Congo hemorrhagic fever virus (CCHFV) is the causative agent of the severe tick-borne, often fatal, zoonotic Crimean-Congo hemorrhagic fever (CCHF), which is widely distributed worldwide. The CCHFV transmission to humans occurs through tick bite, crushing of engorged ticks, or contact with infected host blood. Previously, CCHFV genotype Africa III was reported in Spain. Given the emergence of CCHF and the role of ticks in pathogen maintenance and transmission, we investigated the presence and genotype identity of the virus in tick species parasitizing abundant wild host species in southwestern Spain. A total of 613 adult ticks were collected from hunter-harvested wild ungulates in twenty locations throughout southwestern Spain. Ticks were identified, nucleic acids were extracted, RNA was analysed by a nested RT-PCR targeting CCHFV S segment, and the amplicons were sequenced. According to the 212 bp sequence amplified, the presence of CCHFV human genotype Europe V was detected in Hyalomma lusitanicum and Dermacentor marginatus ticks collected from red deer, fallow deer and Eurasian wild boar in different locations from southwestern Spain. Genotype Africa IV was also detected in a H. lusitanicum tick collected from a red deer. The detection of CCHFV in different tick species collected from various wild hosts and localities provided strong evidence of widespread CCHFV presence in the region, suggesting that the circulation of the virus in Spain requires more attention. Additionally, the identification of the CCHFV genotype Europe V in ticks suggested that its introduction in Spain was probably from Eastern Europe.
Interleukin 16 contributes to gammaherpesvirus pathogenesis by inhibiting viral reactivation

Gammaherpesviruses have evolved various strategies to take advantage of host cellular factors or signaling pathways to establish a lifelong latent infection. Like the human gammaherpesvirus Epstein-Barr virus, murine gammaherpesvirus 68 (MHV68) establishes and maintains latency in the memory B cells during infection of laboratory mice. We have previously shown that MHV68 can immortalize fetal liver-derived B cells that induce lymphomas when injected into immunodeficient mice. Here we identify interleukin 16 (IL16) as a most abundantly expressed cytokine in MHV68-immortalized B cells and show that MHV68 infection elevates IL16 expression. IL16 is not important for MHV68 lytic infection but plays a critical role in MHV68 reactivation from latency. IL16 deficiency increases MHV68 lytic gene expression in MHV68-immortalized B cells and enhances reactivation from splenic latency. Correlatively, IL16 deficiency increases the frequency of MHV68-infected plasma cells that can be attributed to enhanced MHV68 reactivation. Furthermore, similar to TPA-mediated lytic replication of Kaposi's sarcoma-associated herpesvirus, IL16 deficiency markedly induces Tyr705 STAT3 de-phosphorylation and elevates p21 expression, which can be counteracted by the tyrosine phosphatase inhibitor orthovanadate. Importantly, orthovanadate strongly blocks MHV68 lytic gene expression mediated by IL16 deficiency. These data demonstrate that virus-induced IL16 does not directly participate in MHV68 lytic replication, but rather inhibits virus reactivation to facilitate latent infection, in part through the STAT3-p21 axis.
Sterilization Rate of the Axilla After Neoadjuvant Chemotherapy: The Scope for Conservative Surgery

PURPOSE The role of axillary conservation after neoadjuvant chemotherapy (NACT) is debatable. We routinely carry out complete axillary lymph node dissection (ALND). This study was conducted to understand the pathologic axillary complete response (pAxCR) after NACT. MATERIALS AND METHODS We evaluated a prospective database of patients with breast cancer who underwent surgery after NACT in the year 2017 at our institution. NACT was administered to downstage locally advanced breast cancer or facilitate breast-conservation surgery. RESULTS Of 793 patients who underwent surgery after NACT, 97(12.2%) had cN0 disease, 407 (51.3%) had cN1, 262 (32%) had cN2, and 27 (3.4%) had cN3 at presentation. Eighty-eight patients (11.1%) had cT1-2 primary tumor stage, and 623 patients (78.6%) had cT3-4 primary tumor stage; primary tumor stage details were unavailable for 82 patients (10.3%). The median age was 46 years (range, 21-74 years). On histopathology, the overall pAxCR rate was 52.8%. In the cN1 and cN2 settings, 58.7% and 36.6% of patients achieved ypN0 status, respectively. The overall pathologic complete response rate was 22.64% (161 of 711 patients). On univariable analysis, cN stage, histologic grade, hormone receptor status, NACT duration, and lymphovascular invasion were significantly associated with pAxCR (P <.001). On logistic regression, prechemotherapy cN status (odds ratio [OR], 3.08; 95% CI, 2.18 to 4.37; P <.001), estrogen and progesterone receptor status (OR, 0.34; 95% CI, 0.3 to 0.4; P <.001), and administration of both chemotherapy regimens preoperatively (OR, 0.66; 95% CI, 0.45 to 0.97; P <.05) predicted pAxCR. CONCLUSION At least half of patients with cN1 and a third of patients with cN2 breast cancer who develop pAxCR may be suitable candidates for axillary conservation. A careful postchemotherapy assessment followed by a conservative axillary procedure may be an alternative to ALND, but this needs to be studied prospectively.
Importance of Retaining Sufficient Acetabular Depth: Successful 2-Year Outcomes of Hip Arthroscopy for Patients With Pincer Morphology as Compared With Matched Controls

Background: Patients with pincer-type femoroacetabular impingement are commonly treated with arthroscopic reduction of acetabular depth as measured by the lateral center-edge angle (LCEA). The optimal amount of rim reduction has not been established, although large resections may increase contact pressures through the hip. A recent publication demonstrated inferior surgical outcomes in patients with acetabular overcoverage as compared with normal acetabular coverage. Casual observation of our database suggested equivalent improvements, prompting a similar analysis. Purpose: To analyze patient-reported outcomes after hip arthroscopy for femoroacetabular impingement in patients with acetabular overcoverage who were matched with controls with normal coverage, as well as to analyze associations with reduction in LCEA. Study Design: Cohort study; Level of evidence, 3. Methods: Data were collected prospectively from patients with a minimum 2-year follow-up after receiving hip arthroscopy for femoroacetabular impingement by a single surgeon. Cases were reviewed to identify those with pincer-type morphology (LCEA >40°) and matched according to sex, age, chondral damage, and surgery date in a 1:1 ratio with controls with an LCEA of 25° to 40°. The surgical goal was to reduce the LCEA to the upper end of the normal range with minimal rim resection, usually 35° to 37°. Radiographic measurements of coverage, intraoperative findings, procedures, and patient-reported outcomes were recorded, including the 12-Item International Hip Outcome Tool, Non-arthritic Hip Score, Hip Disability and Osteoarthritis Outcome Score, visual analog scale for pain, rates of revision or reoperation, and conversion to total hip arthroplasty. Results: A total of 114 hips (93 patients) for the pincer group were matched 1:1 from 616 hips (541 patients) for the control group. The pincer group (mean ± SD age, 34.5 ± 12.2 years) did not differ in age, body mass index, or follow-up from controls. LCEA was reduced in both groups pre- to postoperatively: the pincer group from 44.0° ± 2.8° to 34.2° ± 3.5° and the controls from 32.9° ± 3.9° to 31.0° ± 3.0°. No differences in improvement were observed: iHOT-12 improved by 35.7 points in both groups (P = .9 for analysis of variance interaction) and Nonarthritic Hip Score by 22.3 points (P = .6). From all eligible surgical procedures, 2-year follow up rates were 2.5% and 2.6% for the pincer and control cohorts, respectively, and 1.2% and 0.3% for conversion to total hip arthroplasty. Conclusion: Arthroscopic management of acetabular overcoverage can achieve excellent results, equivalent to arthroscopy for other causes of symptomatic femoroacetabular impingement. A key finding was smaller rim resections producing a mean postoperative LCEA of 34.2° with a small standard deviation.
Variability in Toxicity of the Dinoflagellate Alexandrium Tamarense Isolated from Hiroshima Bay, Western Japan, as a Reflection of Changing Environmental Conditions

The variability of cellular toxin content in the dinoflagellate Alexandrium tamarense isolated from Hiroshima Bay was analyzed under a variety of culture conditions. Growth and toxicity were represented as a function of light (80, 90, 110, 160 and 350 μmol m -2 s -1 ), temperature (12, 17 and 22°C), salinity (13, 16.5, 19.5, 25, 29, 33, 36.5 and 38 PSU) and ammonium concentration (0.11, 0.22 and 0.44 mM). Toxicity was measured by the tissue culture bioassay using mouse neuroblastoma cells, and expressed as saxitoxin concentration equivalents. Cellular toxicity increased with decreasing salimty. At temperatures of 17 and 22°C, maximum toxin content was observed at the lowest light intensity and growth rate. At the lowest temperature of 12°C, maximum toxin content was observed at intermediate light intensities and growth rates. A drastic increase in toxin content with an increase in ammonium concentration from 0.11 to 0.22 mM supported the idea that ammonium utilization for toxin production direcily brings about a high toxin content in A. tamarense. Our results ecologically imply that the cells become highly toxic in environments with low salinity and high ammonium concentration, and successive cloudy days. Such environmental conditions may lead to increasing risk of shellfish toxification.