bluuebunny/crossref_metadata_2025_split huggingface dataset:
Kinetics of humoral immune response over 17 months of COVID-19 pandemic in a large cohort of healthcare workers in Spain: The ProHEpiC-19 study
Authors: Violán Concepción , Torán Pere , Quirant Bibiana , Lamonja-Vicente Noemi , Carrasco-Ribelles Lucía A , Chacón Carla , Manresa-Dominguez Josep Mª , Ramos-Roure Francesc , Dacosta-Aguayo Rosalia , Palacios Cristina , Roso-Llorach Albert , Pujol Aleix , Ouchi Dan , Monteagudo Mónica , Montero Pilar , Garcia-Sierra Rosa , Arméstar Fernándo , Doladé Maria , Prat Nuria , Bonet Josep Ma , Clotet Bonaventura , Blanco Ignacio , Prado Julia G , Martínez-Cáceres Eva Marái 
Published: February 2022

Abstract
BackgroundUnderstanding the immune response to the SARS-CoV-2 virus is critical for efficient monitoring and defence strategies. The ProHEpic-19 cohort provides a fine-grained description of the kinetics of antibodies after SARS-CoV-2 infection with an exceptional resolution over 17 months.MethodsWe established a cohort of 769 health professionals including healthy and infected with SARS-CoV-2 in northern Barcelona to determine the kinetics of the IgM against the nucleocapsid (N) and the IgG against the N and spike (S) of SARS-CoV-2. We used non-linear mixed models to investigate the kinetics of IgG and IgM measured at nine time points over 17 months from the diagnosis. The model included factors of time, gender, and disease severity (asymptomatic, mild-moderate, severe-critical) to assess their effects and their interactions.Findings: 474 of the 769 participants (61.6%) became infected with SARS-CoV-2. Significant effects of gender and disease severity were found for the levels of all three antibodies. Median IgM(N) levels were already below the positivity threshold in patients with asymptomatic and mild-moderate disease at day 270 after the diagnosis, while IgG(N and S) levels remained positive at least until days 450 and 270, respectively. Kinetic modelling showed a general rise in both IgM(N) and IgG(N) levels up to day 30, followed by a decay with a rate depending on disease severity. IgG(S) levels remained relatively constant from day 15 over time.Interpretation: IgM(N) and IgG(N, S) SARS-CoV-2 antibodies showed a heterogeneous kinetics over the 13 months. Only the IgG(S) showed a stable increase, and the levels and the kinetics of antibodies varied according to disease severity. The kinetics of IgM and IgG observed over a year also varied by clinical spectrum can be very useful for public health policies around vaccination criteria in adult population.Funding: Regional Ministry of Health of the Generalitat de Catalunya (Call COVID19-PoC SLT16_04; NCT04885478)
Factors Affecting Survival in COVID-19 Patients with Genitourinary Cancer
Authors: OzkanOzturk Semra , Kocaman Specialist Zehra , İnal Ali 
Published: February 2022

Abstract
Background: COVID-19 emerged at the end of 2019 and is still one of the most important health problems today. In cancer patients, COVID-19 disease is more severe and fatal. Increased immune system response in COVID-19 leads to increased disease severity and mortality. This study aimed to evaluate the prognostic factors and inflammatory indices in patients with COVID-19 and genitourinary cancer.Methods: This retrospective study included 40 patients diagnosed with genitourinary cancer treated for COVID-19 between April 2020 and July 2021. A total of 27 potential prognostic variables were examined for univariate and multivariate analyzes for survival.Results: A total of 27 variables were analyzed univariable. 3 out of 27 parameters were found to be statistically significant in the univariate analysis: mechanical ventilation requirement (p=0.05), serum fibrinogen level (p=0.046), receiving radiotherapy in the last 28 days (p=0.000). In the multivariate logistic regression analysis; mechanical ventilation requirement independent risk factors for severe COVID-19 in genitourinary cancer (P=0.042).Discussion: In conclusion, mechanical ventilator requirement may be an independent risk factor for prognosis in COVID-19 patients with genitourinary cancer. The increase in fibrinogen due to hypercoagulopathy may be a prognostic independent predictor of survival in patients with genitourinary cancer with COVID-19. Larger, prospective studies are needed.
Sequential Nephron Blockade In Acute Kidney Injury In Critically Ill Patients.
Authors: Samprathi Abhishek , V Padmakumar A , Parekh Aashish 
Published: February 2022

Abstract
Background: Diuretic use in acute kidney injury (AKI) is debatable. Contrasting outcomes have been reported regarding its efficacy in AKI. Sequential nephron blockade (SNB) has never been studied in a diverse ICU population admitted with AKI.Methods: Consecutive patients admitted to medical ICU with oliguric AKI over 1-year period were recruited. SNB as a diuretic strategy was administered. Responders (R) and non-responders (NR) were compared. Demographic data, clinical profile, treatment and outcomes were compared between the groups using t-test and Chi-square test as appropriate. Predictors of mortality were explored using bivariate and multivariate logistic regression analysis and expressed as Odds ratio (OR) with 95% confidence interval (CI).Results: Of the 331 ICU patients admitted with AKI, 312 patients received SNB. The mean (SD) age was 64.14±14·79 years with male preponderance (196:116). Admission SOFA score was significantly (p<0·001) higher (9.6±3.8) in non-responders than responders (6·3±3.6). Overall, 80.13% patients were responders and 19.6% patients received RRT. Significant difference (p<0·001) for diuretic response and dialysis were seen with pre-existing diabetes, higher AKIN stage and SOFA score (>9) at ICU admission, sepsis, shock, mechanical ventilation, positive fluid balance, lengthy ICU stay and mortality. On multivariate logistic regression analysis, SOFA score >9(OR 4.50; 95%CI 2.30-8.80), negative diuretic response (OR 0.45; 95%CI 0.34-0.59), RRT need (OR 1.78; 95%CI 1.25-2.19) and a higher positive fluid balance (OR 2.82; 95%CI 1.76-3.89) were independently associated with death.Conclusions: SNB in oliguric AKI patients resulted in lesser need for dialysis and better outcomes. A negative response, need for dialysis and a higher positive fluid balance were independently associated with mortality.
Assessment of microbiota in the gut and upper respiratory tract associated with SARS-CoV-2 infection
Authors: Li Jiarui , Jing Qiuyu , Li Jie , Hua Mingxi , Di Lin , Song Chuan , Huang Yanyi , Wang Jianbin , Chen Chen , Wu Angela Ruohao 
Published: February 2022

Abstract
Background
The human microbiome plays an important role in modulating the host metabolism and immune system. Connections and interactions have been found between the microbiome of the gut and oral-pharynx in the context of SARS-CoV-2 and other viral infections, hence, to broaden our understanding of host-viral responses in general and to deepen our knowledge of COVID-19, we performed a large-scale, systematic evaluation of the effect of SARS-CoV-2 infection on human microbiota in patients with varying disease severity.
Results
We processed 521 samples from 203 COVID-19 patients with varying disease severity and 94 samples from 31 healthy donors, consisting of 213 pharyngeal swabs, 250 sputum, and 152 faecal samples, and obtained meta-transcriptomes as well as SARS-CoV-2 sequences from each sample. Detailed assessment of these samples revealed altered microbial composition and function in the upper respiratory tract (URT) and gut of COVID-19 patients, and these changes are significantly associated with disease severity. Moreover, URT and gut microbiota show different patterns of alteration, where gut microbiome seems to be more variable and in direct correlation with viral load; and microbial community in upper respiratory tract renders high risk of antibiotic resistance. Longitudinally, microbial composition remains relatively stable during the study period.
Conclusions
Our study has revealed different trends and the relative sensitivity of microbiome in different body sites to SARS-CoV-2 infection. Furthermore, while the use of antibiotics is often essential for prevention and treatment of secondary infections, our results indicate a need to evaluate potential antibiotic resistance in the management of COVID-19 patients in the ongoing pandemic. Moreover, longitudinal follow-up to monitor the restoration of the microbiome could enhance our understanding of the long-term effects of COVID-19.
Quantitatively Assessing Aging Effects In Rapid Motor Behaviours: A Cross-Sectional Study
Authors: Moulton Richard Hugh , Rudie Karen , Dukelow Sean P. , Scott Stephen H. 
Published: February 2022

Abstract
Background: An individual's rapid motor skills allow them to perform many daily activities and are a hallmark of physical health. Although age and sex are both known to affect motor performance, standardized methods for assessing their impact on upper limb function are limited. Methods: Here we perform a cross-sectional study of 643 healthy human participants in two interactive motor tasks developed to quantify sensorimotor abilities, Object-Hit (OH) and Object-Hit-and-Avoid (OHA). The tasks required participants to hit virtual objects with and without the presence of distractor objects. Velocities and positions of hands and objects were recorded by a robotic exoskeleton, allowing motor and cognitive parameters to be calculated for each trial. We verified that these tasks are viable for measuring performance in healthy humans and we examined whether any of the motor or cognitive parameters were related to age or sex. Results: Our analysis shows that both OH and OHA can assess rapid motor behaviours in healthy human participants. It also shows that cognitive parameters in these tasks decline with age, while motor parameters do not. Three cognitive parameters show significant sex-related effects in OH, but these effects disappear in OHA. Conclusions: This study suggests that the underlying effect of aging on rapid motor behaviours is not on the motor system per se, but on the brain's processing rate. Additionally, this study provides a baseline description of healthy human performance in OH and OHA when using these tasks to investigate age-related declines in sensorimotor ability.
A Rare Case of Periprosthetic Streptobacillosis - Rapid Identification via Nanopore Sequencing After Inconclusive VITEK MS Results
Authors: Spott Riccardo , Schleenvoigt Benjamin , Edel Birgit , Pletz Mathias W. , Brandt Christian 
Published: February 2022

Abstract
BackgroundStreptobacillus moniliformis is the main cause of human streptobacillosis, also known as rat-bite or Haverhill fever. Generally transferred by bites or scratches of rats and other rodents or by rat-excrement polluted water, symptoms commonly start to appear after < 10 days and are highly variable. Due to scarcity, non-specific symptoms, and difficulties in cultivating this fastidious organism, the correct diagnosis is frequently delayed.CaseHere, we report an 85-year old male with a left-sided prosthetic hip joint hospitalized because of immobilizing left hip pain. The patient denied fever, chills, and night sweats. There was no swelling or erythema. Via sonography an echo-free round mass was detected at the left hip. Punctuation of the hip joint revealed putrid secretion. From the synovial fluid and from concomitantly drawn blood cultures grew a pleomorphic, gram-negative rod after 48 h and 35 h, respectively. The microorganism formed small, grey, round, and convex colonies. VITEK and VITEK MS (MALDI-TOF) analysis brought no results. Therefore the unknown isolate was sent to the Institute for Infectious Diseases and Infection Control for sequencing. Following isolation, the DNA was sequenced using Nanopore Third-Generation Sequencing. After one hour enough data were generated to identify the microorganism as Streptobacillus moniliformis.ConclusionTo date, this is the second published case of a periprosthetic bone infection caused by Streptobacillus moniliformis. Although streptobacillosis has a mortality rate of around 10% in humans, it is rarely diagnosed and published. In this context, nanopore sequencing enables fast and reliable diagnostic results for identifying microorganisms and their properties.
Predominantly epithelial-type synovial sarcoma with overwhelming neuroendocrine differentiation:a potential diagnostic pitfall
Authors: Chen Ying , Zhou Ning , Guo Deyu , He Xing , Wang Xiaodong , Xu Yujuan 
Published: February 2022

Abstract
Synovial sarcoma is an uncommon tumor of soft tissue, characterized by a specific SS18rearrangement. It generally manifests a lesion composed of monomorphic spindle cells, and can sometimes show variable epithelial differentiation. Predominantly epithelial-type synovial sarcoma is rare and synovial sarcoma with overwhelming neuroendocrine differentiation has never been reported before. Here, we present a case of young man with an epithelial-type synovial sarcoma of the right leg that showed an overwhelming neuroendocrine differentiation. The diagnosis was confirmed by detection of targeted fusion rearrangement associated with synovial sarcoma. This report emphasizes the importance of molecular approaches in modern soft tissue pathology. To avoid misdiagnosis of the tumor such as metastatic neuroendocrine tumor, MPNST with glandular differentiation, and carcinosarcoma, we should understand the expression of neuroendocrine antigens in synovial sarcoma .
A safety study of intraoperative radiation therapy following stereotactic body radiation therapy and multi-agent chemotherapy in the treatment of localized pancreatic adenocarcinoma: study protocol of a phase I trial.
Authors: Reddy Abhinav V. , Hill Colin S. , Zheng Lei , He Jin , Narang Amol K. 
Published: February 2022

Abstract
Background
Localized pancreatic adenocarcinoma carries a poor prognosis even after aggressive therapy. Up to 40% of patients may develop locoregional disease as the first site of failure. As such, there may be a role for intensification of local therapy such as radiation therapy. Radiation dose escalation for pancreatic cancer is limited by proximity of the tumor to the duodenum. However, the duodenum is removed during Whipple procedure, allowing the opportunity to dose escalate with intraoperative radiation therapy (IORT). Although prior studies have shown potential benefit of IORT in pancreatic cancer, these studies did not utilize ablative doses (biologically effective dose [BED10]>100 Gy). Furthermore, the optimal radiation target volume in this setting is unclear. There has been increased interest in a “Triangle Volume” (TV), bordered by the celiac axis, superior mesenteric artery, common hepatic artery, portal vein, and superior mesenteric vein. Dissection of this area, has been advocated for by surgeons from Heidelberg as it contains extra-pancreatic perineural and lymphatic tracts, which may harbor microscopic disease at risk of mediating local failure. Interestingly, a recent analysis from our institution indicated that nearly all local failures occur in the TV. Therefore, the purpose of this protocol is to evaluate the safety of delivering an ablative radiation dose to the TV with IORT following neoadjuvant chemotherapy and stereotactic body radiation therapy (SBRT).
Methods
Patients with non-metastatic pancreatic adenocarcinoma centered in the head or neck of the pancreas will be enrolled. Following treatment with multi-agent neoadjuvant chemotherapy, patients will undergo SBRT (40 Gy/5 fractions) followed by IORT (15 Gy/1 fraction) to the TV during the Whipple procedure. The primary objective is acute (<90 days) toxicity after IORT measured by Clavien-Dindo classification. Secondary objectives include late (>90 days) toxicity after IORT measured by Clavien-Dindo classification, overall survival, local progression-free survival, distant metastasis-free survival, and progression-free survival.
Discussion
If the results show that delivering an ablative radiation dose to the TV with IORT after neoadjuvant chemotherapy and SBRT is safe and feasible, it warrants further investigation in a phase II trial to evaluate efficacy of this approach.
Trial Registration:
This study was registered at ClinicalTrials.gov on 12/2/2021 (NCT05141513). https://clinicaltrials.gov/ct2/show/NCT05141513
Foreign Body: Uncommon Cause of a Catastrophic Upper GI Bleeding: a Case Report
Authors: Nasiri Sara , Ahmadpour Sajjad , Taghavi Ruhollah , Habibi Mohammad Amin , Saeidi Mohammad , Hormati Ahmad , Modarres Mehdi Pezeshgi 
Published: February 2022

Abstract
Background: Upper gastrointestinal bleeding following swallowing foreign body is often caused by a fistula between the large arteries and esophagus, which causes severe and fatal bleeding.Case presentation: A 24-year-old woman presented with severe bleeding in the upper gastrointestinal tract after unwanted swallowing a toothpick. Due to unstable hemodynamic conditions, endoscopic evaluation was not possible, and she was immediately transferred to the operating room. The source of the bleeding was the upper part of the esophagus, as the site of the bleeding was temporarily packed and ceased the surgery. CT-angiography of the head and neck arteries showed esophageal to carotid fistula.Discussion: Esophageal fistula of large arteries usually causes severe bleeding. Awareness from warning signs and timely diagnosis may propose better clinical outcomes.
A surgical case of high-grade urothelial carcinoma of the renal pelvis complicated with giant hydronephrosis, giving rise to diagnostic difficulties on a cytological examination
Authors: Yamada Sohsuke , Takata Mao , Kumagai Motona , Tsubata Yumi , Okanemasa Yoshiiku , Takenaka Michiho , Takenaka Toshie , Yamashita Manabu , Shioya Akihiro 
Published: February 2022

Abstract
Background: We report a surgical case of urothelial carcinoma of the renal pelvis, resulting in diagnostic difficulties on cytological examination. Case Presentation: A man in his late 70s underwent nephrectomy for giant hydronephrosis and renal cysts after nephrostomy and renal cyst puncture and drainage. On all cytological examinations performed before surgery, including nephrostomy urine, renal cyst fluid, catheterized bladder urine, and bladder washings, we were unable to make any conclusive diagnosis of malignancy. The pathological diagnosis of the surgical specimen concluded that this was a case of high-grade urothelial carcinoma of the renal pelvis with focal squamous differentiation (pT4). Liver and lung metastases were identified three months after surgery, and the patient died two months later. Conclusion: It was very difficult to make a conclusive diagnosis using cytological specimens because of the presence of a small number of atypical cells with severe degenerative changes. Since clinicians cannot predict the potential for malignancy on preoperative imaging findings, it is critical to consider the difficulties in clinically making a correct diagnosis of urothelial carcinoma of the upper urinary tract, especially in cases complicated with giant hydronephrosis.
Changes in the Thyroid After Sclerotherapy With Doxycycline
Authors: Raeymaeckers Steven , Tosi Maurizio , Sol Bastiaan , De Mey Johan 
Published: February 2022

Abstract
Background: The literature considers sclerotherapy to be a safe and effective treatment for benign thyroid cysts. No subsequent diagnostic problems have been reported as a complication. We report the occurrence of focal inflammation after said therapy, mimicking a thyroid malignancy.Case presentation: We report a case of a young male with a solitary strongly suspicious lesion in the thyroid. The patient had undergone prior sclerotherapy of a thyroid cyst with Doxycycline. The lesion appeared to be a focal area of inflammation and thus iatrogenic in nature. Systemic use of doxycycline is known to sometimes cause a non-immune chemical thyroiditis, dubbed as black thyroid due to the intense black discoloration of the thyroid. It might be that the instillation of doxycycline was responsible for a similar, more localized, process of affliction.Conclusions: For the work-out of a solitary suspicious thyroid lesion, the medical history of the patient should always be considered. In case of antecedents of ipsilateral sclerotherapy, a reactive inflammatory response may mimic thyroid malignancy. A fine needle aspiration should be performed to exclude thyroid cancer. Treatment is not necessary; the affliction appears self-limiting as evidenced in the follow-up of this case.
Appendiceal Adenocarcinoma Involving the Uterus and Mimicking Primary Endometrial Atypical Gastric-Type Mucinous Proliferation : A Rare Case Report
Authors: Min Qinqin , Lin Xiao , Liang Yingying , Shao Mumin 
Published: February 2022

Abstract
Gastric/gastrointestinal-type mucious lesion in the endometrium may be mostly primary or cervix gastric-type adenocarcinoma involvement. Gastriointestinal and pancreatobiliary adenocarcinoma involving the endometrium is rare. We report a rare appendiceal adenocarcinoma of a 55-year-old female, involving the uterus, mimicking primary endometrial gastric-type lesion. Endometrial lesion was associated with a polyp, which was composed of significant complex papillary architecture and crowed glands resembling lobular endocervical glandular hyperplasia (LEGH), with cytologically abundant pale eosinophilic cytoplasm and atypical nuclear. Mucinous epithelium cells of endometrial lesion was diffusely positive for MUC6, CK7 and negative for p16, PAX8, ER, NapsinA. This histologic morphology and immunophenotype show gastric-type differentiation. Meanwhile, the appendiceal tumor exhibited conventional intestinal type manifestation but focal invasive adenocarcinoma with abundant pale eosinophilic cytoplasm and focally immunoreactivity for MUC6. On the basis of morphologic and immunoreativity examination of the endometrial and appendix, We believe that the diagnosis of atypical mucinous proliferation of gastric-type of endometrium arising from appendiceal adenocarcinoma can be established. Patient died of disease at 3 months after surgery.
Placental DNA methylation changes in the development of gestational diabetes mellitus
Authors: Chen Fujia , Li Min , Fei Xiaoping , Zhu Weiqiang , Zhang Zhaofeng , Shen Yupei , Mao Yanyan , Zhu Qianxi , Xu Jianhua , Zhou Weijin , Du Jing 
Published: February 2022

Abstract
Aims
The aim of this study was to investigate the association between gene methylation alterations and the development of GDM, as well as to investigate the potential epigenetic mechanisms of GDM.
Methods
Reduced representation bisulfite sequencing (RRBS) and RNA sequencing (RNA-seq) analysis were performed on placental tissues from women with GDM and healthy controls. After pyrosequencing, correlation and linear regression analysis were applied based on the effect of methylated-differentially expressed genes (DEGs).
Results
HOXD9, ALDH1A2, CSMD1, TRIM67, and PAX8, five candidate DEGs, were identified. TRIM67 exhibited significant hypermethylation levels at different CpG sites. Hypermethylation of TRIM67 promoter was significantly positively correlated with 1h and 2h OGTT glucose levels and negatively correlated with Lipoprotein(a).
Conclusions
Hypermethylation of the TRIM67 in the placenta of women with GDM may cause insulin resistance, which may correlate with the development of GDM. These findings provide new insights for further studies on the pathophysiology of GDM.