Miracle-dz/UniFAR-FTUs huggingface dataset:
Surface-exposed and soluble calreticulin: conflicting biomarkers for cancer prognosis

ABSTRACT Increased exposure of calreticulin (CALR) on malignant cells is associated with therapy-relevant adaptive immune responses and superior therapeutic outcome in solid tumors and haemato-oncological diseases, because surface-exposed CALR acts as an ‘eat-me’ signal facilitating the phagocytosis of stressed and dying cancer cells by immature dendritic cells, thus favoring antitumor immune responses. On the contrary, mutations of the CALR gene that cause the omission of the C-terminal KDEL endoplasmic reticulum retention motif from CALR protein, resulting in its secretion from cells, act as oncogenic drivers in myeloproliferative neoplasms via the autocrine activation of the thrombopoietin receptor. We recently showed that soluble CALR inhibited the phagocytosis of cancer cells by dendritic cells, thus dampening anticancer immune responses. Furthermore, systemic elevations of soluble CALR that is secreted from tumors or that is artificially supplied by injection of the recombinant protein decreased the efficacy of immunotherapy. Thus, depending on its location, CALR can have immunostimulatory or immunosuppressive functions.
Application of Rare-Earth Elements and Comparison to Molecular Markers in Oil–Source Correlation of Tight Oil: A Case Study of Chang 7 of the Upper Triassic Yanchang Formation in Longdong Area, Ordos Basin, China

The biomarker features of 10 Chang 7 crude oil samples were investigated by gas chromatography–mass spectrometry (GC–MS), and the rare-earth element (REE) compositions of 16 Chang 7 and Chang 8 crude oil samples were determined by inductively coupled plasma–mass spectrometry (ICP–MS) for the first time in Longdong area. Oil–source correlation analysis was improved by biomarkers and REEs. The distribution and relative ratios of a series of biomarker parameters in saturated hydrocarbons and aromatic hydrocarbons of crude oil samples indicate that Chang 7 tight oil has already reached the mature stage. The organic matter mainly comes from lower aquatic organisms of algae, with some contribution of micro-organisms and bacteria, while the forming environment of tight oil is mainly the transitional environment of sub-oxidizing to sub-reducing. The V/(V + Ni) and Ni/Co ratios of crude oil samples suggest that the specific redox conditions of Chang 71 and Chang 72 samples were slightly oxic, while Chang 73 and Chang 8 samples were formed under an anoxic environment. The results of both biomarker-based and REE-based oil–source correlation analysis indicate that Chang 71 and Chang 72 tight oils come from Chang 7 mudstone, while most of the Chang 73 tight oils are from Chang 7 oil shale, with part of mixed from Chang 7 mudstone. This recognition may indicate that Chang 7 mudstone and oil shale are two relatively independent hydrocarbon self-generation and near-storage systems. The analysis results demonstrate that the REE composition in crude oil is an efficient and accurate tool for oil–source correlation in the petroleum system.
Effects of Anesthesia on Postoperative Recurrence and Metastasis of Malignant Tumors

Abstract It is difficult to control the recurrence and metastasis of malignant tumors; furthermore, anesthesia is considered one of the main influencing factors. There has been increasing clinical attention on the effects of anesthetic drugs and methods on postoperative tumor growth and metastasis. We reviewed the effects of anesthesia on tumor recurrence and metastasis; specifically, the effects of anesthetic agents, anesthesia methods, and related factors during the perioperative period on the tumor growth and metastasis were analyzed. This study can provide reference standards for rational anesthesia formulations and cancer-related pain analgesia protocols for surgical procedures in patients with malignant tumors. Moreover, it contributes toward an experimental basis for the improvement and development of novel anesthetic agents and methods.
The Relationship Between Serum 25[OH]D Concentration and Orthopaedic Infection: A Case-Control Study

Background An estimated one in two healthy adults in the United Kingdom suffer from low levels of 25[OH]D. Vitamin D is involved in modulating immune response, but there is less clarity over its role in orthopaedic infection. This study assesses the relationship between serum 25[OH]D concentration and orthopaedic infection. Methods A total of 205 patients in a tertiary referral centre for orthopaedic infection were included in the study. They were divided into groups based on their infection status, matched by age and gender. Data were statistically analysed to determine presence and direction of relationship. Results A total of 114 patients had an infection. There was no statistically significant difference in age or gender between the two groups. Mean serum 25[OH]D concentration was 39 nmol/L in the group with infection and 59 nmol/L in the group without an infection (p<0.01). Overall mean serum 25[OH]D concentration was 48 nmol/L. There was a correlation between low serum 25[OH]D concentration and rate of infection (odds ratio, 5.94; 95% confidence interval [CI], 3.24 to 10.92) with a bivariate correlation of −0.338 (p<0.01). Conclusion This study demonstrates an association between low levels of serum 25[OH]D and increased orthopaedic infection. Orthopaedic inpatients suffered from vitamin D insufficiency, and there was a correlation between higher levels of serum 25[OH]D and lower rates of infection. This suggests that prophylactic supplementation of 25[OH]D may improve outcomes, and provides a foundation for randomized controlled trials to assess its effectiveness in practice.
Comprehensive Analysis of circRNA-miRNA-mRNA Network in Cervical Squamous Cell Carcinoma by Integrated Analysis

Purpose Cervical squamous cell carcinoma (CSCC) seriously affects women’s health worldwide, and it is of great significance to illuminate the specific role of circRNAs in CSCC. Materials and Methods Three mRNA datasets, two miRNA datasets and one circRNA dataset of CSCC, downloaded from GEO, were utilized in this study. Differentially expressed mRNAs (DEmRNAs), miRNAs (DEmiRNAs) and circRNAs (DEcircRNAs) were identified, and a ceRNA (DEcircRNA-DEmiRNA-DEmRNA) regulatory network was constructed. GO and pathway analyses of DEcircRNAs and DEmRNAs in the ceRNA regulatory network were performed. Quantitative real-time polymerase chain reaction (qRT-PCR) validation of the expression of the selected DEmRNAs, DEmiRNAs and DEcircRNAs was performed. Results A total of 1356 DEmRNAs, 13 DEmiRNAs and 77 DEcircRNAs were obtained. The ceRNA network contained 3 circRNA-miRNA pairs and 158 miRNA-mRNA pairs, including 3 circRNAs, 3 miRNAs, and 138 mRNAs. Functional annotation of DEmRNAs in the ceRNA regulatory network revealed that these DEmRNAs were significantly enriched in cell cycle, p53 signalling pathway and DNA replication. The qRT-PCR results were generally consistent with those of our integrated analysis. Conclusion In conclusion, we speculate that the regulation of the hsa_circ_0000069/hsa-miR-125b-5p/CDKN2A and hsa_circ_0020594/hsa-let-7c-5p/CCNB2 axes may be involved in CSCC.
Illustrative Case Series and Narrative Review of Therapeutic Failure of Immunotherapy for Allergic Rhinitis

This is a series of 4 cases (3 therapeutic failure and 1 early relapse) in adult patients treated with allergen immunotherapy (AIT) for allergic rhinitis (AR) in our immunotherapy clinic, which treats 110 new patients per year. AIT includes both subcutaneous and sublingual routes. The current national/international AIT recommendations and the literature have been searched to identify guidance for the optimal management of therapeutic failure of AIT in AR. There is scant information available to support clinicians when treatment failure and/or intolerable side effects occur. The importance is highlighted for developing the guidance and evidence base for the benefit of this patient subgroup. The potential strategies that clinicians have proposed are discussed in this article, though it is acknowledged that these are mostly not evidence-based.
Camera-trap records of breeding Eurasian lynx (Lynx lynx) at the Mount Ilgaz Wildlife Reserve

Breeding seasons are one of the most important periods for the life cycle of large mammals. The young individuals of large carnivore mammals are usually dependent on the female for food and protection. Therefore, availability of the sources and human disturbance at the breeding site are critical for a successful breeding season. The breeding site is of vital importance to the survival of the new-borns and thus to the trends in the population size. The present study assesses the breeding records of the Eurasian lynx (Lynx lynx) based on camera-trapping surveys at the Mount Ilgaz Wildlife Reserve in the province of Kastamonu. The surveys were conducted continuously over a four year period (2014-2018) and the results indicate that the camera-trap stations, which detected the cubs of Eurasian lynx, have also been used by the juvenile individuals of two other top predator large mammals, brown bear (Ursus arctos) and grey wolf (Canis lupus) and the juveniles of their prey species, red deer (Cervus elaphus) and brown hare (Lepus europaeus). Consequently, further assessment of the Wildlife Reserve Area considering the breeding records of the large mammals will contribute to have more effective protection for the Eurasian lynx and other wildlife populations in the Western Black Sea Region of Anatolia.
Some Nursing Screening Tools Can Be Used to Assess High-Risk Older Adults Who Undergo Colorectal Surgery for Cancer

Aim Life expectancy and incidence of cancer among older adults are increasing. The aim of this study was to assess whether routinely used nursing screening tools can predict surgical outcomes in older adults with colorectal cancer. Methods Data of patients who underwent elective colorectal cancer surgery at Rabin Medical Center during the years 2014–2016 were collected retrospectively. Patients were divided into study group (age 80–89 y), and control group (age 60–69 y) for comparing surgical outcomes and six-month mortality. In the study group, screening tool scores were evaluated as potential predictors of surgical outcomes. These included Malnutrition Universal Screening Tool (MUST), Admission Norton Scale Scores (ANSS), Morse Fall Scale (MFS), and Charlson Co-morbidity Index (CCI). Results The study group consisted of 77 patients, and the control group consisted of 129 patients. Postoperative mortality and morbidity were similar in both groups. Nursing screening tools did not predict immediate postoperative outcomes in the study group. MUST and CCI were predictors for six-month mortality. CCI score was 9.43±2.44 in those who died within six months from surgery compared to 7.07 ±1.61 in those who were alive after six months (p<0.05). Post-operative complications were not associated with increased 30-day mortality. Advanced grade complications were associated with an increased six-month mortality (RR=1.37, 95% CI 0.95–1.98, p=0.013). Conclusion Different screening tools for high-risk older adults who are candidates for surgery have been developed, with the caveat of necessitating skilled physicians and resources such as time. Routinely used nursing screening tools may be helpful in better patient selection and informed decision making. These tools, specifically MUST and CCI who were found to predict six-month survival, can be used to additionally identify high-risk patients by the nursing staff and promote further evaluation. This can be a valuable tool in multidisciplinary and patient-centered care.
The Diversity of Midgut Bacteria among Wild-Caught Phlebotomus argentipes (Psychodidae: Phlebotominae), the Vector of Leishmaniasis in Sri Lanka

Phlebotomus argentipes is the main suspected vector for leishmaniasis in Sri Lanka. Investigations on the presence of aerobic bacteria in the gut of sand flies which evidence a potential approach to control leishmaniasis transmission through a paratransgenic strategy are still not available for the local sand fly populations. Field-caught unfed female sand flies collected from three selected Medical Officer of Health (MOH) areas (Polpithigama, Maho, and Galgamuwa) in Kurunegala District, Sri Lanka from August to December 2018 were used. Prokaryotic 16S ribosomal RNA partial gene was amplified and sequenced. Morphological identification revealed the presence of only one sand fly species, P. argentipes (n = 1,969). A total of 20 organisms belonging to two phyla (Proteobactericea and Furmicutes) were detected within the gut microbial community of the studied sand fly specimens. This study documents the first-ever observation of Rhizobium sp. in the midgut of P. argentipes. The presence of Bacillus megaterium, which is considered as a nonpathogenic bacterium with potential use for paratransgenic manipulation of P. argentipes suggest that it may be used as a delivery vehicle to block the vectorial transmission of Leishmania parasites. In addition, Serratia marcescens may be used as a potential candidate to block the parasite development in sand fly vectors since it has evidenced antileishmanial activities in previous investigations. Hence, further studies are required to gain full insight into the potential use of this bacterium in the control of Leishmania parasites through paratransgenesis.
Evaluation of Methods to Measure Condition in Pacific Northwest Larval Lampreys

Abstract Pacific lamprey (Entosphenus tridentatus) populations are declining and western brook lamprey (Lampetra richardsoni) status is unknown in the Pacific Northwest. Accurate measures of fish condition are a basic requirement to monitor health and status of fish populations. Fulton's condition factor has traditionally been used to assess condition of larval lamprey but alternative field-based and laboratory-based measures have not been assessed. We compared condition factor, body density, and lipid content of sympatric larval Pacific lamprey and western brook lamprey in 2010 and 2011 from two rivers of the Pacific Northwest. Condition factor was higher for Pacific lamprey than it was for western brook lamprey. All measures were variable and correlations among condition indices were weak. Body density and lipid content were higher in western brook lamprey in one year suggesting the possibility of increased energy requirements of metamorphosis to a nontrophic adult stage. The body density technique was onerous and likely has little field-based practicality. Body density and lipid content had a negative relationship as increased lipids leads to a more buoyant and less dense fish. Condition factor did not appear to be a good predictor of lipid content in our study and a suite of complex factors, including lipid dynamics prior to metamorphosis and nutritional resources, may underlie these results. This study provides one of the few empirical datasets on sympatric lampreys with different life history strategies.
In silico designing of multi-epitope vaccine construct against human coronavirus infections

Abstract Single stranded RNA viruses were known to cause variety of diseases since many years and are gaining much importance due to pandemic after the identification of a novel corona virus (severe acute respiratory syndrome-coronavirus (SARS-CoV-2)). Seven coronaviruses (CoVs) are known to infect humans and they are OC43 CoV, NL63 CoV, HKU1 CoV, Middle East respiratory syndrome, SARS CoV, and SARS CoV-2. Virus replication weakens the immune system of host thereby altering T-cell count and much of interferon response. Although no vaccine or therapeutic treatment has been approved till now for CoV infection, trials of vaccine against SARS CoV-2 are in progress. One of the epitopes used for vaccine production is of the spike protein on the surface of virus. The work focuses on designing of multi-epitope vaccine construct for treatment of seven human CoV infections using the epitopes present on the spike protein of human CoVs. To address this, immuno-informatics techniques have been employed to design multi-epitope vaccine construct. B- and T-cell epitopes of the spike proteins have been predicted and designed into a multi-epitope vaccine construct. The tertiary structure of the vaccine construct along with the adjuvant has been modelled and the physiochemical properties have been predicted. The multi-epitope vaccine construct has antigenic and non-allergenic property. After validation, refinement and disulphide engineering of the vaccine construct, molecular docking with toll-like receptors (TLRs) have been performed. Molecular dynamics simulation in aqueous environment predicted that the vaccine-TLRs complexes were stable. The vaccine construct is predicted to be able to trigger primary immune response in silico. Communicated by Ramaswamy H. Sarma
Helpfulness of Clinical Visit Summary Content From Multi-Specialty Care: A Mixed-Methods Assessment

Objective: We surveyed patients who visited multiple outpatient specialty practices to understand what summary content was most helpful with the goal of optimizing meaningful outpatient clinical visit summary content. Materials and Methods: We constructed a survey instrument to measure delivery, use, and contents of clinical visit summaries. We surveyed patients who visited with at least 2 different outpatient medical specialties to understand preferences. Results: Most patients in our sample valued the summary information they received, and retained it as healthcare documentation (84%) and/or quick reference in supporting self-care (70%). Patients most commonly reported that information on results of completed tests (91%) and treatment plan instructions (89%) were very helpful. Additionally, patients expressed the importance of online access to clinical visit summary information. Discussion: Most patients used the clinical visit summary as healthcare documentation, and valued online availability of their summary information. Patients most often reported that information on results of recently completed tests and specific instructions on treatment plan were very helpful. Patients who sought further information after their visit most often looked to a provider and/or online. Conclusions: Patients valued clinical visit summary accessibility and as a reference tool to summarize care and provide next steps. Optimal clinical visit summaries might collate and integrate assessments and recommendations from multiple specialties into coherent care plans for patients.
Re-evaluation of essential amino acids in fish by a meta-analytical approach

A meta-analytical evaluation of available data on dose-response to dietary essential amino acids (EAA) in fish from over 177 feeding trials reported in 121 published studies covering about 45 fish species was performed. Weight gain (WG), thermal growth coefficient (TGC) and nitrogen retention (NR) were selected as outcomes to evaluate the optimum requirement value for each EAA. A four parameter saturation kinetic model (SKM – 4 parameter) or a second order polynomial regression analysis (SOPR) were used to model the data sets. The present analysis showed that there exists considerable homogeneity of several data on EAA requirement of fish species included in this study, namely for arginine (Arg), histidine (His), isoleucine (Ile), leucine (Leu), lysine (Lys), methionine (Met), phenylalanine (Phe) and tryptophan (Trp). The SKM – 4 parameter model adjusted well to the compiled data from Lys, Arg, Leu, Ile and Phe dose-response studies, when WG was used as an outcome. Dietary requirement values estimated for His, Met and Trp were achieved through a quadratic model (SOPR), which means that high levels of these EAA in the diet are causing a growth reduction in fish. Available data on valine (Val) and threonine (Thr) from dose-response studies didn't allow the estimation of a requirement value for any of the response criteria used.
Dynamic Hip Screw with Trochanter-Stabilizing Plate Compared with Proximal Femoral Nail Antirotation as a Treatment for Unstable AO/OTA 31-A2 and 31-A3 Intertrochanteric Fractures

Background The dynamic hip screw (DHS) with the addition of an angular stable trochanter-stabilizing plate (TSP) has been considered the ideal treatment for the unstable intertrochanteric fracture type. However, there have been few comparisons between DHS+TSP augmentation with intramedullary (IM) nailing. The aim of this retrospectively registered study was to compare the clinical outcomes of patients with the unstable type of intertrochanteric fractures treated with DHS+TSP or IM nailing (proximal femoral nail antirotation (PFNA)). Methods From June 2013 to April 2018, 358 patients with proximal femur fracture AO/OTA type 31A2 and 31A3 treated with PFNA or DHS+TSP and followed for ≥10 months postoperatively were included. The surgical-dependent outcome evaluation included the operation time, intraoperative blood loss, postoperative decrease in hemoglobin, and blood transfusion amount. Functional status was also measured. Radiographic findings and postoperative complications were recorded and analyzed. Result The operation time was significantly shorter in the DHS+TSP group than that in the PFNA group for both A2 and A3 fractures (A2 type: 84.0 vs.96.4 min; p < 0.05; A3 type: 102.4 vs.116.1 min; p < 0.05). Postoperative decrease in hemoglobin was more significant in the PFNA group than that in the DHS+TSP group for both fracture types (A2 type: −1.88 vs. −1.29 (mg/dL); p < 0.05; A3 type: −1.63 vs. −1.04 (mg/dL); p < 0.05). However, the patients treated with DHS+TSP had significantly more residual pain than those treated with PFNA during the final follow-up (Visual Analog Scale score, A2 type: 28.4 vs.23.2; p < 0.05; A3 type: 27.5 vs.23.6; p < 0.05) and complained of greater implant irritation. Conclusion We found that DHS+TSP was associated with less operation time and less postoperative decrease in hemoglobin but more residual pain and implant irritation than those of PFNA. As a treatment for unstable intertrochanteric fracture, DHS+TSP provided ideal surgical outcomes which were not inferior to the PFNA.
Hyper-Eosinophilic Syndrome Masquerading as Myocardial Infarction, Stroke and Cancer

Hyper-eosinophilic syndrome (HES) can be fatal if left untreated; and it is difficult to make a diagnosis early on due to the symptoms overlapping with many other conditions. For patients presenting with eosinophilia and end-organ damage, clinicians should have a high degree of suspicion for HES. Treatment with steroids can prevent further progression or can lead to complete resolution of the symptoms.