bluuebunny/crossref_metadata_2025_split huggingface dataset:
BamQuery: a proteogenomic tool to explore the immunopeptidome and prioritize actionable tumor antigens
Authors: Cuevas Maria Virginia Ruiz , Hardy Marie-Pierre , Larouche Jean-David , Apavaloaei Anca , Kina Eralda , Vincent Krystel , Gendron Patrick , Laverdure Jean-Philippe , Durette Chantal , Thibault Pierre , Lemieux Sébastien , Perreault Claude , Ehx Grégory 
Published: August 2023

AbstractMHC-I-associated peptides deriving from non-coding genomic regions and mutations can generate tumor-specific antigens, including neoantigens. Quantifying tumor-specific antigens’ RNA expression in malignant and benign tissues is critical for discriminating actionable targets. We present BamQuery, a tool attributing an exhaustive RNA expression to MHC-I-associated peptides of any origin from bulk and single-cell RNA-sequencing data. We show that many cryptic and mutated tumor-specific antigens can derive from multiple discrete genomic regions, abundantly expressed in normal tissues. BamQuery can also be used to predict MHC-I-associated peptides immunogenicity and identify actionable tumor-specific antigens de novo.
Governance of rangeland in Bhutan: Institutions and policy initiatives
Authors: Wangchuk Kesang , Wangdi Jigme , Dorji Tashi 
Published: August 2023

AbstractHigh-altitude rangelands support the economies of mountain communities in the Himalayas. This article highlights institutions and policy initiatives for good governance of rangelands in Bhutan and draws lessons from previous efforts to mainstream rangeland development. Both formal and informal institutions support the rangeland governance in Bhutan. The article elaborates on critical rangeland-related amendments to the Bhutanese Land Act. Rangeland stewardship and access rights are outlined, along with alternative governance approaches that rely on pastoralists’ traditions and indigenous knowledge. It highlights concerns and disputes about using and managing rangelands and explains traditional institutions and practices of conflict resolution. The article’s final section discusses the challenges of rangeland governance and the aspirations of herding communities under the new Land Act. Rangeland owners have reconciled with the amendments to the Act. They are willing to work with the government to implement the Act’s provisions and bring the desired reforms in rangeland governance.
Microbiological quality of some packed and unpacked bread products in Alexandria, Egypt
Authors: Ali Manal A. , Hashish Mona H. , Fekry Marwa M. 
Published: August 2023

Abstract
Background
Bakery products are important food snacks consumed by people of all ages and economic groups. The growth of unwanted microorganisms that deteriorate products such as bacteria, moulds, and fungi in these foodstuffs may offer risks to consumers’ health and generate considerable economic losses. This work aimed to assess the microbiological quality of some packed and unpacked bread products in Alexandria, Egypt.

Methods
This cross-sectional comparative study involved 168 local and branded bakery products that were collected randomly from 2 districts in Alexandria. Hygienic practices such as covering of the bread and wearing gloves during handling were observed and recorded. All bread samples were tested to determine the total plate count (TPC), presence/absence of Staphylococcus aureus (S. aureus), total yeasts and moulds in CFU/g and total coliform count (TC) in MPN/g.

Results
The mean of the total yeasts and moulds and TC in the packed bread was lower than that of the unpacked bread (3.40 × 103 CFU/g and 3.25 MPN/g versus 6.37 × 103 CFU/g and 31.61 MPN/g, respectively). However, the mean of TPC in the packed bread was higher than that of the unpacked bread (1.39 × 106versus 2.07 × 105 CFU/g, respectively). The mean TPC, total yeasts and moulds and TC was higher in the studied flatbread than Fino bread and toast (3.4 × 106, 1.14 × 104 CFU/g and 24.6 MPN/g, respectively). The presence of S. aureus was higher in flat, unpacked bread, bread displayed outside the shop and handled without gloves.

Conclusion
Bread produced by local bakeries showed lower standards in packaging and microbial quality. Better manufacturing, packaging, storage, and handling initiatives should be introduced to avoid related food safety concerns in the future. The formal authorities should define and clarify standards and rules on bread safety.
Diagnostic performance of US LI-RADS in hepatocellular carcinoma surveillance
Authors: Abduljabbar Ahmed Haitham , Wazzan Mohammad A. 
Published: August 2023

Abstract
Background
Liver cirrhosis and chronic infection with hepatitis B virus are major risk factors for hepatocellular carcinoma (HCC). Guidelines recommend ultrasound (US) surveillance for population at risk of HCC. The US Liver Imaging Reporting and Data System (LI-RADS) aims at standardization of interpretation, reporting, and management recommendations for US surveillance examinations. The aim of this study is to assess the diagnostic accuracy of US LI-RADS in early HCC detection in patients at risk.

Results
This retrospective study included patients with surveillance US between January 2018 and January 2020 who had a contrast-enhanced CT or MRI of the liver within 1 month from the date of US examination. Visualization scores and US categories were assigned according to the US LI-RADS lexicon. A total of 264 participants were eligible for the study. HCC was diagnosed in 33 participants. The US-3 category had a 39.4% sensitivity and 93.5% specificity for HCC detection. The US-2 category had a 45.4% sensitivity and 87% specificity for HCC detection. The visualization score C showed the highest number of HCC (19/33) and had the highest false-negative rate (76%, 13 of 17).

Conclusions
Both US-2 and US-3 categories showed high specificity and low sensitivity for HCC detection in the setting of surveillance of patients at high risk. Visualization score C had the highest risk for HCC and the highest rate of false-negative results. Intense surveillance by contrast-enhanced CT or MRI might be beneficial for patients with limited visualization scores B and C.
Lower back pain caused by radiculopathy induced by lumbar stenosis - literature review
Authors: Turek Michał , Winiarz Aleksandra , Szlendak Paula , Toś Katarzyna , Wojtala Kacper , Grosman Sylwia , Węgrzyniak Agata , Drobek Dominik , Wąsala Katarzyna , Wokurka Wojciech 
Published: August 2023

Introduction: Lumbar spine pain is a common clinical problem. Due to the multitude of causes of pain, it is important to know the most common ones in order to choose an effective method of treatment.
The aim of this study: Summary of current knowledge regarding back pain caused by radiculopathy associated with lumbar stenosis.
Material and method: The review includes publications published in 1995-2020. The search of the publications in the Pubmed database was carried out using the following keywords: back pain, radiculopathy, lumbar stenosis.
Description of the stage of the knowledge: Lumbar radiculopathy caused by lumbar stenosis is a common clinical problem, especially in older age groups. In diagnostics, an interview with the patient, physical examination and imaging tests - especially CT and MRI - are important. In most patients, conservative treatment is sufficient - the use of analgesics and anti-inflammatory drugs and physiotherapy. In justified cases, surgical treatment should be considered as the most effective causative treatment of the disease. In the last 20 years, the availability of both diagnostic methods has increased and new surgical techniques have appeared, aiming at minimally invasive treatment.
Summary: Radiculopathy caused by lumbar stenosis is a contributing factor to the occurrence of pain, which can hinder the normal functioning of the patient.Proper diagnosis, identification of the impact and methods of treatment, both conservative and surgical, can help the patient and affect his quality of life. Early diagnosis and treatment are crucial for the effective treatment of pain associated with radiculopathy caused by lumbar stenosis.
use of psilocybin in the treatment of psychiatric disorders – review
Authors: Woźniak Justyna , Bogacz Rafał , Gaik Magdalena , Uram Ewa , Magda Inga , Womperski Karol , Osuch Magdalena 
Published: August 2023

Introduction: The word “psychedelic” derives from the Greek language and can be loosely translated as “mind manifesting” which is to convey that these substances allow the mind to unleash its hidden potential. Psilocybin is considered to be a “classic psychedelic” and is most commonly found in the form of so-called “magic mushrooms”. Due to its unique properties psilocybin has been used during religious ceremonies and rituals for centuries and more recently also explored in a medical context. Nowadays many studies are being carried out to prove the efficacy of its use in the treatment of various psychiatric disorders.
Aim of study: Review of the current knowledge on the subject of psilocybin applied in the treatment of psychiatric disorders, such as major depressive disorder, treatment-resistant depression and addiction.
Methods and materials: A review of chosen literature was carried out in the PubMed database and Google Scholar using the following phrases: psilocybin, psychedelics, psychedelic-assisted therapy, major depressive disorder, addiction.
Results: Recent studies suggest that psilocybin may be an effective form of treatment for cancer-related psychiatric distress, treatment-resistant depression and addiction. There are some reports of psilocybin being useful when treating obsessive-compulsive disorder and cluster headaches.
Conclusions: More large-scale, randomized, placebo-controlled studies are required to prove these promising findings. Psychological support is crucial during the treatment with psilocybin.
Prediction of fracture nonunion leading to secondary surgery in patients with distal femur fractures
Authors: Sainio Heini , Rämö Lasse , Reito Aleksi , Silvasti-Lundell Marja , Lindahl Jan 
Published: August 2023

AimsSeveral previously identified patient-, injury-, and treatment-related factors are associated with the development of nonunion in distal femur fractures. However, the predictive value of these factors is not well defined. We aimed to assess the predictive ability of previously identified risk factors in the development of nonunion leading to secondary surgery in distal femur fractures.MethodsWe conducted a retrospective cohort study of adult patients with traumatic distal femur fracture treated with lateral locking plate between 2009 and 2018. The patients who underwent secondary surgery due to fracture healing problem or plate failure were considered having nonunion. Background knowledge of risk factors of distal femur fracture nonunion based on previous literature was used to form an initial set of variables. A logistic regression model was used with previously identified patient- and injury-related variables (age, sex, BMI, diabetes, smoking, periprosthetic fracture, open fracture, trauma energy, fracture zone length, fracture comminution, medial side comminution) in the first analysis and with treatment-related variables (different surgeon-controlled factors, e.g. plate length, screw placement, and proximal fixation) in the second analysis to predict the nonunion leading to secondary surgery in distal femur fractures.ResultsWe were able to include 299 fractures in 291 patients. Altogether, 31/299 fractures (10%) developed nonunion. In the first analysis, pseudo-R2 was 0.27 and area under the receiver operating characteristic curve (AUC) was 0.81. BMI was the most important variable in the prediction. In the second analysis, pseudo-R2 was 0.06 and AUC was 0.67. Plate length was the most important variable in the prediction.ConclusionThe model including patient- and injury-related factors had moderate fit and predictive ability in the prediction of distal femur fracture nonunion leading to secondary surgery. BMI was the most important variable in prediction of nonunion. Surgeon-controlled factors had a minor role in prediction of nonunion.Cite this article: Bone Jt Open 2023;4(8):584–593.
Switchable metasurface for high-efficiency absorption and broadband polarization conversion based on vanadium dioxide in the terahertz frequency
Authors: Xie Shenglin , Zhu Hailiang , Zhou Yuxin , Yu Miao , Mou Jinchao , Liu Lin , Di Yujie , Wang Gengchen 
Published: August 2023

High-performance devices with superior execution will facilitate the practical
application of terahertz (THz) technology and foster
THz innovation. In this paper, taking advantage of the phase
transition characteristics of vanadium dioxide (VO2), a reconfigurable metasurface with
absorption and polarization conversion capacities is proposed. The
metallic condition of VO2 results in the formation of a
wideband absorber. It provides more than 90% absorption over a broad
spectral range from 3.32 to 5.30 THz. Due to the regularity of
the meta-atom, the absorber is not polarization-delicate and keeps a
high retention rate in the scope of incoming angles from 0° to 45°.
When VO2 is in the insulating condition, the
calculated outcomes demonstrate that the cross-polarization conversion
rate can reach more than 90% in the range of 2.29–7.85 THz when x-polarized or y-polarized waves are incident
vertically. The proposed metasurface is likely to be used in the
fields of emitters, sensors, imaging systems, and wireless
communication.
Follow-up evaluation of pulmonary function and computed tomography findings in chronic kidney disease patients after COVID-19 infection
Authors: Jaturapisanukul Solos , Yuangtrakul Nadwipa , Wangcharoenrung Dearada , Kanchanarat Krongkan , Radeesri Kan , Maneerit Jakravoot , Manomaipiboon Anan , Rojtangkom Khemika , Ananthanalapa Chompoonuth , Rungrojthanakit Siwaporn , Thinpangnga Peerawit , Alvior Joshua , Trakarnvanich Thananda 
Published: August 2023

Pulmonary complications are common after SARS-CoV2- infection. However, data on pulmonary sequelae of COVID-19 after recovery in dialysis patients are limited. We determined the prevalence of abnormal lung function tests and CT findings and investigate the association factors impacting pulmonary dysfunction. This prospective observational cohort study enrolled 100 patients with stage 5 chronic kidney disease (CKD) undergoing dialysis who had recovered from COVID-19 for ≥3 months. Pulmonary function test (PFT) and chest computed tomography (CT) were performed. Demographic data and laboratory results were recorded. The mean patient age was 55.15 ± 12.84 years. Twenty-one patients (21%) had severe COVID-19, requiring mechanical ventilation or oxygen supplementation. Pulmonary function tests revealed a restrictive pattern in 41% (95% confidence interval [CI], 31.73–50.78;) and an obstructive pattern in 7.29% (95% CI, 3.19–13.25) patients. The severe group showed PFT test results similar to the non-severe group, with three patients showing severe obstructive lung disease. The CT scan findings included reticulation (64%), multifocal parenchymal band (43%), ground glass opacities (32%), and bronchiectasis (28%). The median total CT score was 3 (interquartile range, 1–8.5). The CT score and PFT findings showed no association with pulmonary dysfunction extent, except in bronchiectasis. Lung function indices were associated with abnormal CT findings. Abnormal CT findings (bronchiectasis, reticulation, and ground-glass opacities) was associated with higher oxygen requirements than normal CT findings (p = 0.008, bronchiectasis; p = 0.041, reticulation; p = 0.032, ground-glass appearance). Aside from CT findings and CRP levels, no significant lung abnormalities were observed in severe and non-severe patients. Some patients had residual symptoms at follow-up. The findings indicate persistence of both radiological and physiological abnormalities in dialysis patients after COVID-19. However, the prevalence of these abnormalities was comparable to that in the normal population; few patients experienced ongoing symptoms. Follow-up observations and evaluations are warranted.
Trial registration. Clinicaltrials.gov Identifier: NCT05348759.
Patient safety improvement in the gastroenterology department: An action research
Authors: Sadeghi Amir , Masjedi Arani Abbas , Karami Khaman Hosna , Qadimi Arezoo , Ghafouri Raziyeh 
Published: August 2023

Background
Patient safety is a global concern. Safe and effective care can shorten hospital stays and prevent or minimize unintentional harm to patients. Therefore, it is necessary to continuously monitor and improve patient safety in all medical environments. This study is aimed at improving patient safety in gastroenterology departments.

Methods
The study was carried out as action research. The participants were patients, nurses and doctors of the gastroenterology department of Ayatollah Taleghani Hospital in Tehran in 2021–2022. Data were collected using questionnaires (medication adherence tool, patient education effectiveness evaluation checklist, and medication evidence-based checklist), individual interviews and focus groups. The quantitative data analysis was done using SPSS (v.20) and qualitative data analysis was done through content analysis method using MAXQDA analytic pro 2022 software.

Results
The majority of errors were related to medication and the patient’s fault due to their lack of education and prevention strategy were active supervision, modification of clinical processes, improvement of patient education, and promotion of error reporting culture. The findings of the research showed that the presence of an active supervisor led to the identification and prevention of more errors (P<0.01). Regarding the improvement of clinical processes, elimination of reworks can increase satisfaction in nurses (P<0.01). In terms of patient education, the difference was not statistically significant (P>0.01); however, the mean medication adherence score was significantly different (P<0.01).

Conclusion
The improvement strategies of patient safety in Gastroenterology department included the modification of ward monitoring processes, improving/modification clinical processes, improvement of patient education, and development of error reporting culture. Identifying inappropriate processes and adjusting them based on the opinion of the stakeholders, proper patient education regarding self-care, careful monitoring using appropriate checklists, and presence of a supervisor in the departments can be effective in reducing the incidence rate. A comprehensive error reporting program provides an opportunity for employees to report errors.
Association between affective temperaments and psychosomatic symptoms in women with Hashimoto’s thyroiditis
Authors: Stanić Gordana , Marinković Snežana , Milin Lazović Jelena , Ignjatović Ristić Dragana 
Published: August 2023

Background
Hashimoto’s thyroiditis (HT) is a prevalent autoimmune disease of thyroid gland with a shared immunological mechanism with mood disorders. Affective temperament (AT) is a biologically determined personality trait that has been linked to mood disorders. The aim of this study was to examine the association between dominant AT and levels of psychosomatic symptoms in women newly diagnosed with HT in comparison to clinically healthy subjects.

Methods
The observational cross-sectional study with nested case control study was involving 146 consecutive participants, who were divided into three groups. The two study groups consisted of women with HT (73), including 49 with hypothyroid HT and 24 with euthyroid HT, and the third group was a control group of healthy participants (73). The Serbian version of the TEMPS-A was utilized to assess AT, while the 4DSQ was used to measure psychosomatic symptoms.

Results
The results showed that hyperthymic AT was dominant in all examined groups. The groups with HT differed from the control group in terms of depressive and cyclothymic AT. Furthermore, the study found higher levels of psychosomatic symptoms in the group with HT compared to the control group, with significant differences in distress (p = 0.005) and somatization (p = 0.023) levels. All AT was associated with levels of psychosomatic symptoms in subjects with hypothyroid HT. In contrast, in subjects with euthyroid HT, the association was only found between depressive and cyclothymic AT with distress and depression levels, as well as between somatization and cyclothymic AT. No association was found between AT and anxiety levels in subjects with euthyroid HT.

Conclusion
The research found differences between study groups in the association between AT and levels of psychosomatic symptoms. Further research with a larger sample size is necessary to more clearly define the associations between affective temperaments and psychosomatic symptoms in women with euthyroid and hypothyroid HT.
Long term prophylactic anticoagulation for portal vein thrombosis after splenectomy: A systematic review and meta-analysis
Authors: Liao Zheng , Wang Zixiang , Su Chenguang , Pei Yinxuan , Li Weiwei , Liu Jinlong 
Published: August 2023

Aim
The aim of this study was to evaluate the efficacy and safety of the anticoagulants for the prevention of portal vein system thrombosis (PVST) in patients with cirrhosis after splenectomy and explore the optimal time of anticoagulant administration.

Methods
A systematic literature search was performed using PubMed, Embase and China Biology Medicine disc (CBM)databases, so as to screen out studies comparing the prognoses between cirrhotic post-splenectomy patients treated with and without anticoagulants. The parameters that were analyzed included the incidence of PVST and postoperative bleeding.

Results
With a total of 592 subjects, we included 8 studies (6 observational and 2 randomized trials) that fulfilled the inclusion criteria. We found that the incidence of PVST was significantly lower in the anticoagulation group during the first 6 months of anticoagulant administration. And the largest difference in the incidence of PVST between the anticoagulation and control groups was observed at 3 months (odds ratio 0.17(0.11~0.27); P = 0.767; I2 = 0.0%) and 6 months (OR = 0.21(0.11~0.40); P = 0.714; I2 = 0.0%) postoperatively. The incidence of bleeding was not significantly higher in the anticoagulation group (odds ratio 0.71 (0.30~1.71); P = 0.580; I2 = 0.0%).

Conclusion
Low-molecular weight heparin (LMWH) and warfarin can decrease the incidence of PVST in post-splenectomy cirrhotic patients without an increased risk of bleeding. And the optimal use time of warfarin is 6 months after splenectomy.
High-temperature corrosion behavior of S30432 in high-efficiency ultra-supercritical boiler burning low-alkali and high-sulfur coal
Authors: Liu Yugang , Liu Yinhe , Mo Chunhong , Ran Shenming , Yin Chaoqiang 
Published: August 2023

Abstract
In this study, the resistance of S30432 to low-alkali coal ash corrosion in a high-efficiency USC boiler was investigated. Currently, S30432 is widely used in the high-temperature superheater and reheater of boilers burning low-alkali and high-sulfur coal. During the experiment, S30432 coated with low-alkali coal ash were fixed in a high-temperature tubular reactor, and hot gas at 650 °C and 700 °C containing SO2 passed over the specimens for 2000 h. Then the specimens were tested by X-ray diffraction, scanning electron microscopy, and energy-dispersive spectroscopy. It was found that S30432 specimens mainly underwent high-temperature oxidation. For the gas temperature of 700 °C and SO2 volume concentration of 0.35 %, the sulfidation reaction occurred and the weight change was only 1.08 mg cm−2. The results show that there is no obvious high-temperature corrosion after three years of operation of a 700 MW 620 °C boiler. The results are in contrast with the high-alkali coal ash corrosion resistance of S30432. It is concluded that S30432 can meet the requirements of a high-efficiency USC boiler burning low-alkali and high-sulfur coal.