Miracle-dz/UniFAR-FTUs huggingface dataset:
Algorithm Selection as a Collaborative Filtering Problem

Focusing on portfolio algorithm selection, this paper presents a hybrid machine learning approach, combining collaborative filtering and surrogate latent factor modeling. Collaborative filtering, popularized by the Netflix challenge, aims at selecting the items that a user will most probably like, based on the previous movies she liked, and the movies that have been liked by other users. As first noted by Stern et al (2010), algorithm selection can be formalized as a collaborative filtering problem, by considering that a problem instance ''prefers'' the algorithms with better performance {on this particular instance}. A main difference between collaborative filtering approaches and mainstream algorithm selection is to extract latent features to describe problem instances and algorithms, whereas algorithm selection most often relies on the initial descriptive features. A main contribution of the present paper concerns the so-called cold-start issue, when facing a brand new instance. In contrast with Stern et al. (2010), ARS learns a non-linear mapping from the initial features onto the latent features, thereby supporting the recommendation of a good algorithm for the new problem instance with constant computational cost. The experimental validation of ARS considers the domain of constraint programming (2008 CSP and 2011 SAT competition benchmarks) and gradient-free continuous optimization (black-box optimization benchmarks), demonstrating the merits and the genericity of the method.
Self-weighted NOSER-prior electrical impedance tomography using internal electrodes in cardiac radiofrequency ablation

Objective: Radiofrequency (RF) cardiac ablation is a commonly used method for treating cardiac arrhythmias in which the information of the dynamic lesion heating is critical to cardiologists but is currently lacking. Electrical impedance tomography (EIT) is a temporal modality of imaging the changes in the electrical properties within a measured object and hence might be able to track the electrical variation due to temperature changes within the myocardium. Within this paper, (1) a time-efficient algorithm with self-weighted NOSER-prior and (2) a measurement filtering process for optimizing the number of measurement were proposed for monitoring the lesion size during the cardiac RF ablation, taking advantage of internal catheter-based electrodes and the prior information of anatomical structure and the catheter location, which are usually available during the ablation course. Approach: A tank model with a circular myocardium of 12 mm in thickness, 16 external electrodes on the boundary and three internal catheter-based electrodes positioned inside the endocardium were made. The ablations were simulated using Pennes’ bioheat transfer equation and the simulated temperature gradients were then transferred to EIT measurements. The algorithm used one reference ablation for its optimization and then was tested with numerous 90 s ablations containing three disturbances: the catheter location mapping, the wide range of varied myocardium conductivity and the blood’s cooling convection, and the Gaussian noises with 10–40 µV in standard deviation. Main results: The results showed that, with the optimized number of 55 measurements, the algorithm still performed well when dealing with all three disturbances plus the random noises up 25 µV. Specifically, the lesion depth and width were measured within 1.6 mm and 3.2 mm in error respectively in at least 80% out of 100 simulated ablations. Significance: The algorithm has successfully measured the lesion size with good accuracy and tolerances of noise and other system perturbations. More tests in vitro and in vivo are required in the future to confirm the algorithm’s feasibility.
Inflammatory Bowel Disease: A Stressed “Gut/Feeling”

Inflammatory bowel disease (IBD) is a chronic and relapsing intestinal inflammatory condition, hallmarked by a disturbance in the bidirectional interaction between gut and brain. In general, the gut/brain axis involves direct and/or indirect communication via the central and enteric nervous system, host innate immune system, and particularly the gut microbiota. This complex interaction implies that IBD is a complex multifactorial disease. There is increasing evidence that stress adversely affects the gut/microbiota/brain axis by altering intestinal mucosa permeability and cytokine secretion, thereby influencing the relapse risk and disease severity of IBD. Given the recurrent nature, therapeutic strategies particularly aim at achieving and maintaining remission of the disease. Alternatively, these strategies focus on preventing permanent bowel damage and concomitant long-term complications. In this review, we discuss the gut/microbiota/brain interplay with respect to chronic inflammation of the gastrointestinal tract and particularly shed light on the role of stress. Hence, we evaluated the therapeutic impact of stress management in IBD.
Efficacy and safety of apatinib plus docetaxel as the second or above line treatment in advanced nonsquamous NSCLC

Abstract Background: Apatinib is an oral small-molecule tyrosine kinase inhibitor targeting vascular endothelial growth factor receptor 2 (VEGFR-2). Some clinical trials have demonstrated that apatinib is efficacious against advanced nonsquamous NSCLC. Objective: This study aimed to probe efficacy and safety of apatinib plus docetaxel, as the second or above line treatment, in advanced nonsquamous NSCLC. Design: Multicenter, prospective, single arm study. Setting: Three teaching hospitals centers in the Sichuan. Participants: Fourteen patients with stage IVA/B nonsquamous NSCLC had previously received at least 1 platinum-based chemotherapy regimen. Intervention: Patients who were enrolled between November 2016 and January 2018 were given docetaxel (75 mg/m2, i.v., d1) plus oral apatinib (250 mg/d), 4 weeks as one cycle, until disease progression or intolerance to adverse events (AE). Main outcome measures: The primary endpoint was progression-free survival (PFS). The secondary endpoints comprised objective response rate (ORR), disease control rate (DCR), overall survival (OS), and AE incidence rate. Results: All patients carried adenocarcinoma by pathological type. The median follow-up duration was 9.76 months. Out of 14 cases, 12 were evaluable, showing ORR of 33.33%, DCR of 66.67%, DCR of 50% in cases with brain metastasis, median PFS of 2.92 months (95% CI: 1.38–4.48), and 6-month OS of 80%. Primary AEs encompassed: leukopenia in 7 cases (58.33%), hand-foot skin reaction in 5 cases (41.67%), and diarrhea in 4 cases (33.33%). Among them, grade 3 AEs were: leukopenia in 4 cases (33.33%), and hand-foot skin reaction in 1 case (8.33%). No grade 4/5 AEs were reported. Univariate and multivariate analysis were conducted respectively for PFS and OS. These factors encompassed: gender, age, gene mutations, clinical stage, ECOG scores, quantity of metastatic foci, brain metastasis, and hand-foot skin reaction. Results demonstrated zero risk factors for PFS or OS. Conclusion: Apatinib plus docetaxel, as the second or above line treatment, is effective and safe against advanced nonsquamous NSCLC, with good tolerance profile. Trial registration: NCT03416231.
Altered structural brain network resulting from white matter injury in obstructive sleep apnea.

STUDY OBJECTIVES To assess, using fractional anisotropy (FA) analysis, alterations of brain network connectivity in adults with obstructive sleep apnea (OSA). Abnormal networks could mediate clinical functional deficits and reflect brain tissue injury. METHODS Structural brain networks were constructed using diffusion tensor imaging (DTI) from 165 healthy (age 57.99 ± 6.02 years, male 27.9%) and 135 OSA participants (age 59.01 ± 5.91 years, male 28.9%) and global network properties (strength, global efficiency, and local efficiency) and regional efficiency were compared between groups. We examined MRI biomarkers of brain tissue injury using FA analysis and its effect on the network properties. RESULTS Differences between groups of interest were noted in global network properties (p-value < 0.05, corrected), and regional efficiency (p-value < 0.05, corrected) in the left middle cingulate and paracingulate gyri, right posterior cingulate gyrus, and amygdala. In FA analysis, OSA participants showed lower FA values in white matter (WM) of the right transverse temporal, anterior cingulate and paracingulate gyri, and left postcentral, middle frontal and medial frontal gyri, and the putamen. After culling fiber tracts through WM which showed significant differences in FA, we observed no group difference in network properties. CONCLUSIONS Changes in WM integrity and structural connectivity are present in OSA participants. We found that the integrity of WM affected brain network properties. Brain network analysis may improve understanding of neurocognitive deficits in OSA, enable longitudinal tracking, and provides explanations for specific symptoms and recovery kinetics.
Soil Water Sensor Performance and Corrections with Multiple Installation Orientations and Depths under Three Agricultural Irrigation Treatments

Performance evaluations and corrections of soil water sensors have not been studied using different installation orientations under various irrigation treatments in the Texas High Plains. This study evaluated the performance of four sensors using factory calibration and derived field corrections as compared to calibrated neutron moisture meters (NMMs). Sensor performance was assessed using horizontal insertion, laid horizontal placement, and vertical insertion at 15.2, 45.7, and 76.2 cm depths in a clay loam soil with three irrigation treatments. Results indicated the factory-calibrated Acclima 315 L performed satisfactorily using horizontal insertion as compared to NMM measurements at 45.7 and 76.2 cm depths with a ±2% mean difference (MD) and <3.5% root mean square error (RMSE). The factory-calibrated Acclima 315 L using horizontal insertion also performed satisfactorily across all irrigation treatments according to soil profile water storage (MD = 0.36% and RMSE = 3.25%). Generally, the factory-calibrated Decagon GS1 and Campbell Scientific 655 using vertical insertion agreed more closely with NMM measurements compared with other installation orientations. There was a significant underestimation of water storage (>60 mm) in the 0.9 m soil profile using the Watermark 200SS. In summary, field corrections are required for Decagon GS1, Campbell Scientific 655, and Watermark 200SS sensors.
Real world experience of R‐CHOP with or without consolidative radiotherapy vs DA‐EPOCH‐R in the first‐line treatment of primary mediastinal B‐cell lymphoma

Primary mediastinal large B‐cell lymphoma (PMBCL) is a distinct clinico‐pathological subtype of diffuse large B‐cell lymphoma with unclear prognostic factors and limited clinical data. Optimal treatment and role for radiotherapy is not fully defined. We performed a multicenter retrospective review of 124 patients with newly diagnosed PMBCL between 2001 and 2016. Treatment regimens were R‐CHOP (n = 41), R‐CHOP + RT (n = 37), and DA‐EPOCH‐R (n = 46). 6% (n = 3) in the DA‐EPOCH‐R group received RT. With a median follow up of 45 months, the overall 5‐year OS and PFS was 89.4% and 82.4%, respectively. The type of chemo‐radiotherapy regimen, B symptoms and Ann‐Arbor staging showed a significant association with OS on univariate analysis but only B symptoms remained prognostic (P = 0.012) after multivariate analysis. The chemo‐radiotherapy regimen, Japanese IPI and Ann‐Arbor stage was significantly associated with PFS in univariate analysis, but only chemo‐radiotherapy regimen remained significant (P = 0.02) after multivariate analysis. Patients who received R‐CHOP + RT or DA‐EPOCH‐R had better PFS than those receiving R‐CHOP alone, with 5‐year PFS of 90% vs 88.5% vs 56%, respectively (P = 0.02). In the subgroup analysis of patients with bulk (n = 71), R‐CHOP alone (n = 21) had inferior 5‐year PFS 56.6% compared to those who received R‐CHOP + RT (n = 23) 91.3% or DA‐EPOCH‐R (n = 27) 92.6% (P = 0.007). In contrast, in patients without bulk (n = 42), there was no impact of treatment regimen on PFS (P = 0.25). In conclusion, R‐CHOP + RT and DA‐EPOCH‐R provide excellent outcomes in patients with PMBCL. In patients with bulky disease, the use of DA‐EPOCH‐R may be preferable as it allows omission of RT without reduction in efficacy.
Whole-blood DNA Methylation Markers for Risk Stratification in Colorectal Cancer Screening: A Systematic Review

DNA methylation profiles within whole-blood samples have been reported to be associated with colorectal cancer (CRC) occurrence and might enable risk stratification for CRC. We systematically reviewed and summarized studies addressing the association of whole-blood DNA methylation markers and risk of developing CRC or its precursors. We searched PubMed and ISI Web of Knowledge to identify relevant studies published until 12th November 2018. Two reviewers independently extracted data on study population characteristics, candidate genes, methylation measurement methods, methylation levels of patients in comparison to healthy controls, p-values, and odds ratios of the markers. Overall, 19 studies reporting 102 methylation markers for risk assessment of colorectal neoplasms met our inclusion criteria. The studies mostly used Methylation Specific Polymerase Chain Reaction (MS-PCR) for assessing the methylation status of a defined set of genes. Only two studies applied array-based genome-wide assays to assess the methylation levels. Five studies incorporated panels consisting of 2–10 individual methylation markers to assess their potential for stratifying the risk of developing colorectal neoplasms. However, none of these associations was confirmed in an independent cohort. In conclusion, whole-blood DNA methylation markers may be useful as biomarkers for risk stratification in CRC screening, but reproducible risk prediction algorithms are yet to be established by large scale epigenome-wide studies with thorough validation of results in prospective study cohorts including large screening populations. The possibilities of enhancing predictive power by combining methylation data with polygenetic risk scores and environmental risk factors need to be explored.
Epidemiology of Interpersonal Trauma among Women and Men Psychiatric Inpatients: A Population-Based Study

Objective: Small clinical samples suggest that psychiatric inpatients report a lifetime history of interpersonal trauma. Since past experiences of trauma may complicate prognosis and treatment trajectories, population-level knowledge is needed about its prevalence and correlates among inpatients. Methods: Using health-administrative databases comprising all adult psychiatric inpatients in Ontario, Canada (2009 to 2016, n = 160,436, 49% women), we identified those who reported experiencing physical, sexual, and/or emotional trauma in their lifetime, 1 year, and 30 days preceding admission. We described the prevalence of each type of trauma, comparing women and men using modified Poisson regression, and identified individual-level characteristics associated with lifetime trauma history using multivariable logistic regression. Results: 31.7% of inpatients reported experiencing trauma prior to admission. Lifetime prevalence was higher in women (39.6% vs. 24.1%; age-adjusted prevalence ratio [aPR] = 1.68; 95% CI, 1.65 to 1.71), including sexual (22.7% vs. 8.4%; aPR = 2.81; 95% CI, 2.73 to 2.89), emotional (33.3% vs. 19.4%; aPR = 1.76; 95% CI, 1.72 to 1.79), and physical trauma (24.2% vs. 14.8%; aPR = 1.68; 95% CI, 1.65 to 1.72). Factors most prominently associated with lifetime trauma were witnessing parental substance use (adjusted odds ratio [aOR] = 8.68; 95% CI, 8.39 to 8.99), female sex (aOR = 2.29; 95% CI, 2.23 to 2.35), and number of recent stressful life events (aOR = 1.62; 95% CI, 1.59 to 1.65). Conclusions: These results suggest that trauma-informed approaches are essential to consider in the design and delivery of inpatient psychiatric services for both women and men.
Chronic prostatitis/pelvic pain syndrome: MRI findings and clinical correlations

We aimed to evaluate whether pelvic magnetic resonance imaging (MRI) could play a role in better assessing chronic pelvic pain syndrome. We evaluated 44 male patients (median 41 aged) with a clinical history of painful pelvic symptoms, lasting for at least three of the previous 6 months, associated with urinary, anorectal and sexual disorders in the absence of bacterial prostate infection. All these patients underwent ultrasound (US) and MRI evaluation of the pelvis. Prostate imaging findings, such as gland morphology evaluated by US and prostatic signal intensity on MRI, appeared normal in the majority of patients (38/44; 82%). Extraparenchymal alterations were found in 28 patients (63.6%); the most frequent was the dilatation of periprostatic vein plexus (20/28; 71.4%), significantly correlated to chronic pelvic pain syndrome (p = 0.0013), regardless of different clinical presentations. This finding was tested in a control group of 90 patients, demonstrating an excellent specificity (97%), good positive predictive value (87%) and diagnostic accuracy (80%). MRI confirmed its high capability in evaluating prostatic and extraprostatic structures. Periprostatic vein dilatation, which identified approximately two‐thirds of the patients with chronic pelvic pain syndrome using pelvic MRI, significantly correlated to chronic pelvic pain syndrome, independently of patient age, symptoms and prostatic volume.
Comparing the content and quality of video, telephone, and face-to-face consultations: a non-randomised, quasi-experimental, exploratory study in UK primary care

Background Growing demands on primary care services have led to policymakers promoting video consultations (VCs) to replace routine face-to-face consultations (FTFCs) in general practice. Aim To explore the content, quality, and patient experience of VC, telephone (TC), and FTFCs in general practice. Design and setting Comparison of audio-recordings of follow-up consultations in UK primary care. Method Primary care clinicians were provided with video-consulting equipment. Participating patients required a smartphone, tablet, or computer with camera. Clinicians invited patients requiring a follow-up consultation to choose a VC, TC, or FTFC. Consultations were audio-recorded and analysed for content and quality. Participant experience was explored in post-consultation questionnaires. Case notes were reviewed for NHS resource use. Results Of the recordings, 149/163 were suitable for analysis. VC recruits were younger, and more experienced in communicating online. FTFCs were longer than VCs (mean difference +3.7 minutes, 95% confidence interval [CI] = 2.1 to 5.2) or TCs (+4.1 minutes, 95% CI = 2.6 to 5.5). On average, patients raised fewer problems in VCs (mean 1.5, standard deviation [SD] 0.8) compared with FTFCs (mean 2.1, SD 1.1) and demonstrated fewer instances of information giving by clinicians and patients. FTFCs scored higher than VCs and TCs on consultation-quality items. Conclusion VC may be suitable for simple problems not requiring physical examination. VC, in terms of consultation length, content, and quality, appeared similar to TC. Both approaches appeared less ‘information rich’ than FTFC. Technical problems were common and, though patients really liked VC, infrastructure issues would need to be addressed before the technology and approach can be mainstreamed in primary care.
Current Therapeutic Options in the Treatment of Rheumatoid Arthritis

Rheumatoid arthritis (RA) is a systemic autoimmune disease characterized by chronic inflammation of the joints. Untreated RA leads to a destruction of joints through the erosion of cartilage and bone. The loss of physical function is the consequence. Early treatment is important to control disease activity and to prevent joint destruction. Nowadays, different classes of drugs with different modes of action are available to control the inflammation and to achieve remission. In this review, we want to discuss differences and similarities of these different drugs.
Cystathionine-Gamma-Lyase-Derived Hydrogen Sulfide-Regulated Substance P Modulates Liver Sieve Fenestrations in Caecal Ligation and Puncture-Induced Sepsis

Cystathionine-γ-lyase (CSE) is a hydrogen sulfide (H2S)-synthesizing enzyme that promotes inflammation by upregulating H2S in sepsis. Liver sinusoidal endothelial cells (LSECs) are fenestrated endothelial cells (liver sieve) that undergo alteration during sepsis and H2S plays a role in this process. Substance P (SP) is encoded by the preprotachykinin A (PPTA) gene, and promotes inflammation in sepsis; however, its regulation by H2S is poorly understood. Furthermore, the interaction between H2S and SP in modulating LSEC fenestrations following sepsis remains unclear. This study aimed to investigate whether CSE/H2S regulates SP and the neurokinin-1 receptor (NK-1R) and modulates fenestrations in LSECs following caecal ligation and puncture (CLP)-induced sepsis. Here we report that the absence of either CSE or H2S protects against liver sieve defenestration and gaps formation in LSECs in sepsis by decreased SP-NK-1R signaling. Following sepsis, there is an increased expression of liver CSE and H2S synthesis, and plasma H2S levels, which were aligned with higher SP levels in the liver, lungs and plasma and NK-1R in the liver and lungs. The genetic deletion of CSE led to decreased sepsis-induced SP and NK-1R in the liver, lungs and plasma SP suggesting H2S synthesized through CSE regulates the SP-NK-1R pathway in sepsis. Further, mice deficient in the SP-encoding gene (PPTA) preserved sepsis-induced LSEC defenestration and gaps formation, as seen by maintenance of patent fenestrations and fewer gaps. In conclusion, CSE/H2S regulates SP-NK-1R and modulates LSEC fenestrations in sepsis.
American Masters Road Running Records—The Performance Gap Between Female and Male Age Group Runners from 5 Km to 6 Days Running

Recent studies investigating elite and master athletes in pool- and long-distance open-water swimming showed for elite swimmers that the fastest women were able to outperform the fastest men, and for master athletes that elderly women were able to achieve a similar performance to elderly men. The present study investigating age group records in runners from 5 km to 6 days aimed to test this hypothesis for master runners. Data from the American Master Road Running Records were analyzed, for 5 km, 8 km, 10 km, 10 miles, 20 km, half-marathon, 25 km, 30 km, marathon, 50 km, 50 miles, 100 km, 100 miles, 12 h, 24 h, 48 h and 144 h, for athletes in age groups ranging from 40 to 99 years old. The performance gap between men and women showed higher effects in events lengthening from 5 km to 10 miles (d = 0.617) and lower effects in events lengthening from 12 to 144 h (d = 0.304) running. Both other groups showed similar effects, being 20 km to the marathon (d = 0.607) and 50 km to 100 miles (d = 0.563). The performance gap between men and women showed higher effects in the age groups 85 years and above (d = 0.953) followed by 55 to 69 years (d = 0.633), and lower effects for the age groups 40 to 54 years (d = 0.558) and 70 to 84 years (d = 0.508). In summary, men are faster than women in American road running events, however, the sex gap decreases with increasing age but not with increasing event length.