Miracle-dz/UniFAR-FTUs huggingface dataset:
When are Deep Networks really better than Decision Forests at small sample sizes, and how?

Deep networks and decision forests (such as random forests and gradient boosted trees) are the leading machine learning methods for structured and tabular data, respectively. Many papers have empirically compared large numbers of classifiers on one or two different domains (e.g., on 100 different tabular data settings). However, a careful conceptual and empirical comparison of these two strategies using the most contemporary best practices has yet to be performed. Conceptually, we illustrate that both can be profitably viewed as"partition and vote"schemes. Specifically, the representation space that they both learn is a partitioning of feature space into a union of convex polytopes. For inference, each decides on the basis of votes from the activated nodes. This formulation allows for a unified basic understanding of the relationship between these methods. Empirically, we compare these two strategies on hundreds of tabular data settings, as well as several vision and auditory settings. Our focus is on datasets with at most 10,000 samples, which represent a large fraction of scientific and biomedical datasets. In general, we found forests to excel at tabular and structured data (vision and audition) with small sample sizes, whereas deep nets performed better on structured data with larger sample sizes. This suggests that further gains in both scenarios may be realized via further combining aspects of forests and networks. We will continue revising this technical report in the coming months with updated results.
Evaluation of Gender Inequity in Thyroid Cancer Diagnosis

Key Points Question How does thyroid cancer risk vary by sex? Findings The cohort study in this comparison study found that the current ratio of small (≤2 cm) papillary thyroid cancer (PTC) incidence in women to men is 4.39:1, and the meta-analysis found that pooled odds ratio of subclinical PTC at autopsy in women compared with men is 1.07. The incidence rate ratio decreased as cancer lethality increased; and thyroid cancer mortality ratio by sex (women to men) was 1.02:1. Meaning Gender differences in thyroid cancer are mostly confined to the detection of small PTCs; the incidence of more lethal types of thyroid cancer, thyroid cancer mortality, and subclinical cancer are similar by gender.
Dual Modulation of Osteoclast Differentiation by Lipopolysaccharide

ABSTRACTLipopolysaccharide (LPS) modulates bone resorption by augmentation of osteoclastogenesis. It increases inosteoblasts the production of RANKL, interleukin (IL)-1, prostaglandin E 2 (PGE 2 ), and TNF- , each knownto induce osteoclast activity, viability, and differentiation. We examined the role of direct interactions of LPSwith osteoclast precursors in promoting their differentiation. To this end, we have used bone marrowmononuclear cell preparations in the absence of osteoblasts or stromal cells. We found that LPS does notinduce osteoclast differentiation in these cells. Moreover, the inclusion of LPS blocked the osteoclastogenicactivity of RANKL. However, LPS is a potent inducer of osteoclastogenesis in RANKL-pretreated cells, evenif present in the absence of exogenous RANKL. Osteoprotegerin (OPG) does not affect the stimulatory phaseof LPS modulation of osteoclastogenesis, ruling out involvement of endogenous RANKL. LPS induces theexpression of TNF- and IL-1 in osteoclast precursors, regardless if they were or were not pretreated withRANKL. These two cytokines induced osteoclast differentiation in RANKL-pretreated cells. To examine ifthese cytokines mediate LPS effect in an autocrine mechanism, we measured the effect of their neutralizationon LPS osteoclastogenic activity. Although neutralization of IL-1 did not affect LPS activity, a markedinhibition was observed when TNF- was neutralized. However, TNF- expression was increased also inconditions in which LPS inhibited RANKL osteoclastogenic activity. We found that LPS reduces the expres-sion of RANK and macrophage colony—stimulating factor (M-CSF) receptor. In summary, LPS impacts onosteoclastogenesis also via its interactions with the precursor cells. LPS inhibits RANKL activity by reducingthe expression of RANK and M-CSF receptor and stimulates osteoclastogenesis in RANKL-pretreated cells viaTNF- . (J Bone Miner Res 2002;17:1211–1218)Key words: osteoclast, TNF, lipopolysaccharide, RANKL, macrophage colony–stimulating factor receptorINTRODUCTION
Cross-sectional study of pediatric pain prevalence, assessment, and treatment at a Canadian tertiary hospital

ABSTRACT Background Painful experiences are common among hospitalized children. Long-term negative biopsychosocial consequences of undertreated pain are recognized. Aims The study benchmarks pain prevalence, assessment, and treatment as first steps to improve pain care in a Canadian tertiary hospital. Methods Single-day audits were undertaken on the pediatric ward (PW), pediatric emergency department (ED), and maternal services (MS). Participants (child or caregiver proxy) reported hospital pain experiences in the preceding 24 h; medical records were reviewed for assessment and treatment. Results Among 84 participants, pain prevalence ranged from 75% to 88%; mean pain intensity ranged from 5.7 to 6.5/10. Prevalence of moderate to severe pain was 78% on PW, 65% in ED, and 55% on MS; needle pokes were the most frequent cause of worst pain. Documentation of pain assessment varied by setting (PW, 93%; ED, 13%; MS, 0%). Documented maximum pain scores were significantly lower compared to participant report (mean difference 4.5/10, SD 3.1, P < 0.0001). A total 29% (6/21) of infants with heel lance or injection received breastfeeding or sucrose, and 29% (7/24) of participants receiving other needle procedures had documented or reported topical lidocaine use. All participants on MS underwent needle procedures. Conclusions Pain is experienced commonly by infants and children in PW, ED, and MS. Pain assessment documentation is not routine and underestimates participant report. Evidence-based pain management strategies are underutilized. An institution-wide quality improvement approach is required to address pain care. Pain assessment and needle pain prevention and treatment should be prioritized in these pediatric acute care and newborn care settings.
Increased Levels of CD107a and Intracellular Cytokines in IL-2 Stimulated PBMCs from Endometriosis Patients

It has been postulated that the immune system is impaired in individuals with endometriosis, with attention directed to natural killer (NK) cells. Specifically, it has been hypothesized that altered numbers of peripheral NK cells in blood are associated with the presence of endometriotic lesions. This study aimed to evaluate the level of the peripheral NK cell surface marker CD107a in endometriosis in the presence of IL-2 stimulation. Peripheral blood mononuclear cells (PBMCs) were obtained from 7 women with endometriosis and 7 women without endometriosis. The PBMCs were divided into two groups and either treated with recombinant IL-2 or left untreated. The cytotoxic activity of the PBMCs toward target cells (K562) was evaluated. Then, both groups were cocultured for 4 days. The expressions of CD107a, TNF-α, and IFN-γ were determined using flow cytometry analysis. There was no difference in the expression of CD107a prior to IL-2 stimulation in PBMCs from women with endometriosis compared to those from women without endometriosis. However, we observed upregulation of the expression of the surface marker CD107a after treatment in the endometriosis group. In addition, there was a significant difference in CD107a expression in the endometriosis group before versus after stimulation with IL-2 (p < 0.01). We also found no difference in the production of TNF-α and IFN-γ before versus after treatment with IL-2 in either groups. The levels of CD107a were significantly enhanced in peripheral blood taken from women with endometriosis after treatment with IL-2.
The Acceptance Rate Toward COVID-19 Vaccine in Africa: A Systematic Review and Meta-analysis

Background: The Coronavirus Disease 2019 (COVID-19) pandemic remains serious public issue. COVID-19 vaccine is a vital strategy to prevent this critical pandemic. However, unwillingness to take this vaccine are key barriers to manage the COVID-19 pandemic. The control of this pandemic will depend principally on the people acceptance of COVID-19 vaccine. Therefore, this systematic review and meta-analysis was intended to determine the acceptance rate toward COVID-19 vaccine in Africa. Methods: African Journals OnLine, PubMed, Cochrane Review, HINARI, EMBASE, Google Scholar, Web of Science, and Scopus were used to retrieve related articles. The Preferred Reporting Items for Systematic Review and Meta-Analysis (PRISMA) guidelines were used for this study. Random-effect model, a funnel plot, Egger’s test, I2 statistic, subgroup analysis was done. The study was performed by using a STATA version 11 statistical software. Results: A total of 22 studies with 33,912 study participants were included in this systematic review and meta-analysis. From this finding, the pooled prevalence of acceptance toward COVID-19 vaccine among adults in Africa was 48.93% (95% CI: [39.49, 58.37]). The subgroup analysis revealed that the pooled prevalence of COVID-19 vaccine acceptance among adults in Africa was highest (66.03%, 95% CI [62.84, 69.22]) in Southern Africa, and Lowest (24.28%, 95% CI [3.26, 45.30]) in Northern Africa. Conclusion: This study showed that the estimate of the pooled prevalence of acceptance toward COVID-19 vaccine among adults in Africa was very low. All concerned bodies should be actively involved to improve the acceptance rate of COVID-19 vaccine.
Impact of High Serum Levels of MMP-7, MMP-9, TGF-β and PDGF Macrophage Activation Markers on Severity of COVID-19 in Obese-Diabetic Patients

Objective The aim of this study was to identify an association between the severity of COVID-19 in obese-diabetic patients and altered serum levels of MMP-7, MMP-9, TGF-β, and PDGF macrophage activation markers. Methodology The study included 70 COVID-19 patients, divided into two groups: Group 1 included: Obese COVID-19 patients with type 2 diabetes mellitus (T2D, n=22 patients) and group 2 included; non-obese, non-diabetic COVID-19 patients as an age- and sex-matched control group (n=48 patients). Serum levels of the tested biomarkers were measured by ELISA at admission and after one weak follow-up. Results There was a significant reduction in the serum levels of LBP in obese-diabetic COVID-19 patients versus the control group (8.34±3.94 vs 20.78±7.61) (p 0.0001). Significant elevation of MMP-7, MMP-9, PDGF and TGF-β was detected in obese diabetic COVID-19 patients compared to the non-obese non-diabetic group: 1044.7±519.6 vs 405.6±164.1, 483.05±46.5 vs 173.31±76.26, 154.5±62.78 vs 39.77±21.52, and 603.05±258.82 vs 180.29±97.17, respectively. The serum levels of macrophage activation markers in obese-diabetic patients one week after admission revealed that patients with acute respiratory distress syndrome (ARDS) had significantly higher serum levels of MMP-7 and MMP-9 than non-ARDS patients (p 0.02 and p 0.01 respectively). Conclusion Macrophages were mainly polarized towards the M2 phenotype in obese-diabetic COVID-19 patients with significant upregulation of the pro-fibrotic markers MMP-7, MMP-9, PDGF, and TGF-β. Thus, high levels of MMP-7 and MMP-9 are associated with ARDS in severe COVID-19 disease among obese-diabetic patients.
Extracellular Vesicles in Bone Tumors: How to Seed in the Surroundings Molecular Information for Malignant Transformation and Progression

Bone is a very dynamic tissue hosting different cell types whose functions are regulated by a plethora of membrane-bound and soluble molecules. Intercellular communication was recently demonstrated to be also sustained by the exchange of extracellular vesicles (EVs). These are cell-derived nanosized structures shuttling biologically active molecules, such as nucleic acids and proteins. The bone microenvironment is a preferential site of primary and metastatic tumors, in which cancer cells find a fertile soil to “seed and blossom”. Nowadays, many oncogenic processes are recognized to be sustained by EVs. For example, EVs can directly fuel the vicious cycle in the bone/bone marrow microenvironment. EVs create a favourable environment for tumor growth by affecting osteoblasts, osteoclasts, osteocytes, adipocytes, leukocytes, and endothelial cells. At the same time other crucial tumor-mediated events, such as the premetastatic niche formation, tumor cell dormancy, as well as drug resistance, have been described to be fostered by tumor-derived EVs. In this review, we will discuss the main body of literature describing how the cancer cells use the EVs for their growth into the bone and for educating the bone microenvironment to host metastases.
Mediators and Theories of Change in Psychotherapy for Young People With Personality Disorders: A Systematic Review Protocol

Background: Personality disorders (PDs) are a severe health issue already prevalent among adolescents and young adults. Early detection and intervention offer the opportunity to reduce disease burden and chronicity of symptoms and to enhance long-term functional outcomes. While psychological treatments for PDs have been shown to be effective for young people, the mediators and specific change mechanisms of treatment are still unclear. Aim: As part of the “European Network of Individualized Psychotherapy Treatment of Young People with Mental Disorders” (TREATme), funded by the European Cooperation in Science and Technology (COST), we will conduct a systematic review to summarize the existing knowledge on mediators of treatment outcome and theories of change in psychotherapy for young people with personality disorders. In particular, we will evaluate whether mediators appear to be common or specific to particular age groups, treatment models, or outcome domains (e.g., psychosocial functioning, life quality, and adverse treatment effects). Method: We will follow the reporting guidelines of the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) statement recommendations. Electronic databases (PubMed and PsycINFO) have been systematically searched for prospective, longitudinal, and case–control designs of psychological treatment studies, which examine mediators published in English. Participants will be young people between 10 and 30years of age who suffer from subclinical personality symptoms or have a personality disorder diagnosis and receive an intervention that aims at preventing, ameliorating, and/or treating psychological problems. Results: The results will be published in a peer-reviewed journal and at conference presentations and will be shared with relevant stakeholder groups. The data set will be made available to other research groups following recommendations of the open science initiative. Databases with the systematic search will be made openly available following open science initiatives. The review has been registered in PROSPERO (evaluation is pending, registration number ID 248959). Implications: This review will deliver a comprehensive overview on the empirical basis to contribute to the further development of psychological treatments for young people with personality disorders.
Enhanced Efficacy of Some Antibiotics in Presence of Silver Nanoparticles Against Multidrug Resistant Pseudomonas aeruginosa Recovered From Burn Wound Infections

Burn wound infections with multidrug-resistant (MDR) bacteria are shown in many countries as severe widespread health threats. Consequently, attention has been devoted to new nanoparticle-based materials in the field of antimicrobial chemotherapy for burn wound infections. This study aimed to evaluate both in vitro and in vivo efficacies of nanoparticle–antibiotic combinations as new classes of materials subjected against MDR Pseudomonas aeruginosa. Out of 40 Gram-negative isolates, 23 P. aeruginosa were recovered from patients with burn wound infections attending different hospitals in Tanta, Egypt. The susceptibility test revealed that 95.7% of P. aeruginosa isolates were MDR with a high incidence of resistance against carbenicillin. Antibacterial activities of silver nanoparticles (Ag-NPs) against the isolates examined showed various inhibition zone diameters ranging from 11 to 17 mm. Strong synergistic efficacy of neomycin was reported in combination with Ag-NPs against MDR P. aeruginosa P8 and P14 isolates. The in vivo effectiveness of various pharmaceutical formulations prepared from a combination of neomycin antibiotic with Ag-NPs in the treatment of induced bacterially infected mice burns showed that maximum healing activity along with faster wound contraction reported with the combination of neomycin-Ag-NPs in the spray formulation. Generally, data indicated that incorporating Ag-NPs in combination with certain antibiotics may be a new, promising application for wound treatments, especially burns infected with MDR P. aeruginosa.
Numerical Study of Evaporation and Motion Characteristics of Liquid Nitrogen Droplet in High-Speed Gas Flow

In the cryogenic wind tunnel, cooling the circulating gas to cryogenic temperature by spraying liquid nitrogen (LN2) is an efficient way to increase the Reynolds number. The evaporation and motion of LN2 droplets in the high-speed gas flow is the critical process that determines the cooling rate, cooling capacity and the safe operation of the down-stream compressor. In this study, a numerical model of droplet motion and evaporation in high-speed gas flow is developed and verified against experimental data. The droplet evaporation rate, diameter and velocity are obtained during the evaporation process under different gas temperatures and flow velocities. The results show that the gas temperature has dominant influence on the droplet evaporation rate. High flow speed can increase droplet evaporation effectively at the beginning process. Evaporation of droplets with different diameters follows a similar trend. The absolute evaporation rate increases with the increase of droplet diameter while the relative evaporation amount is highest for the smallest droplet due to its high area-volume ratio. This numerical study provides insight for understanding the evaporation of LN2 droplets in high-speed gas flow and useful guidelines for the design of LN2 spray cooling.
A Single Institution Retrospective Study of Palliative Radiotherapy for Bone Metastases: Comparing the First Six Months of the 2020 Covid-19 Pandemic with the Same Calendar Period during 2019

Synchronous double primary malignancies of lymphoma and thyroid cancer are rare. In this retrospective study, we investigated the pathology, clinical characteristics, and treatment outcomes of patients with synchronous lymphoma and thyroid cancer. Of the 1156 newly diagnosed lymphoma patients treated in our hospital between January 1, 2016 and February 1, 2021, 8 cases had lymphoma complicated with thyroid cancer. The clinical data and treatment strategies of 8 cases with synchronous lymphoma and thyroid cancer were retrospectively analyzed. The median age of patients was 56 (25–64) years. All the 8 patients were female and papillary thyroid cancer. Only 1 patient had peripheral T-cell lymphoma, and the other 7 were B-cell lymphoma. Seven of 8 patients had normal free triiodothyronine and free thyroxine at the time of diagnosis. Seven thyroid cancer patients received total thyroidectomy and levothyroxine and the remaining 1 patient has a plan for surgery. At the last follow-up, 7 patients with B-cell lymphoma are alive; the patient with peripheral T-cell lymphoma complicated with thyroid cancer died due to lymphoma progression. Synchronous lymphoma and thyroid cancer are more predominant in women. Histologically, B-cell lymphomas and papillary thyroid cancer subtypes are more common. Attention should be paid to the presence of thyroid nodules in the diagnosis of lymphoma. Biopsy or ultrasound-guided fine needle aspiration of the suspicious thyroid nodule should be performed to exclude thyroid malignancy. Abbreviations: CR = complete remission, DLBCL = diffuse large B-cell lymphoma, DPM = double primary malignancies, HL = Hodgkin lymphoma, MALT = mucosa-associated lymphoid tissue, PET-CT = positron emission tomography-computed tomography.
A database-based approach for predicting coupled cascade reaction kinetics in polymers: application to oxidative degradation kinetics of high-performance polymers

Abstract Coupled cascade reactions forming complex reaction networks can be commonly found in polymerisation reactions and other reactions involving radical intermediates. Predicting the mechanism and kinetics of such reactions requires proper modelling of complex reaction networks. This becomes particularly difficult when coupled cascade reactions occur in polymeric systems containing different types of residues. Here, we propose a residue-based database approach to model such reactions in polymers, with the aid of a visual interface developed here. We demonstrate this approach by predicting the oxidative degradation kinetics of high-performance polymers (HPPs). First, we show that residue-based reaction database can be linked to construct the whole reaction network. For this purpose, we developed a database for oxidation reactions of commonly occurring residues in industrially important HPPs. Then we implement a visual interface which takes inputs from a user about residues in a polymer of interest and subsequently link appropriate databases to build reaction network. Finally, this program executes numerical integration of rate equations in the back-end. Application of this approach and the developed program is demonstrated by studying the oxidative degradation kinetics of three well-known HPPs- PMR-15, HFPE-30 and PMR-II, where the computations took less than a minute in a conventional desktop computer.
Parasitic nematodes of the genus Syphacia Seurat, 1916 infecting Cricetidae in the British Isles: the enigmatic status of Syphacia nigeriana

Abstract Abstract Oxyurid nematodes (Syphacia spp.) from bank (Myodes glareolus) and field/common (Microtus spp.) voles, from disparate geographical sites in the British Isles, were examined morphologically and genetically. The genetic signatures of 118 new isolates are provided, based primarily on the rDNA internal transcribed spacers (ITS1-5.8S-ITS2) region and for representative isolates also on the small subunit 18S rDNA region and cytochrome c oxidase subunit 1 (cox-1) gene locus. Genetic data on worms recovered from Microtus spp. from the European mainland and from other rodent genera from the Palaearctic, North America and West Africa are also included. We test historical hypotheses indicating that S. nigeriana is a generalist species, infecting a range of different rodent genera. Our results establish that S. nigeriana is a parasite of both bank and field voles in the British Isles. An identical genotype was also recorded from Hubert's multimammate mouse (Mastomys huberti) from Senegal, but Mastomys spp. from West Africa were additionally parasitized by a related, although genetically distinct Syphacia species. We found no evidence for S. petrusewiczi in voles from the British Isles but isolates from Russia and North America were genetically distinct and formed their own separate deep branch in maximum likelihood molecular phylogenetic trees.