bluuebunny/crossref_metadata_2025_split huggingface dataset:
Discordance of retroperitoneal and thoracic histologic findings in patients with metastatic germ cell tumors at postchemotherapy residual tumor resection
Authors: Che Yue , Wöltjen Carolin , Lusch Achim , Winter Christian , Trainer Stephan , Schirren Moritz , Sponholz Stefan , Knoefel Wolfram Trudo , Albers Peter , Hiester Andreas 
Published: July 2024

Abstract
Introduction and objectives
Postchemotherapy residual tumor resection (PC-RTR) is an important part of the multimodal treatment for patients with metastatic germ cell tumors. Simultaneous retroperitoneal and thoracic metastases often require consecutive surgical procedures. This study analyzes the histologic findings after abdominal and thoracic surgery in order to tailor the sequence and intensity of surgery.

Patients and methods
From a total of 671 PC-RTRs from 2008 to 2021 we analyzed 50 patients with stage III non-seminomatous germ cell tumor (NSGCT) who had undergone both retroperitoneal and thoracic postchemotherapy residual tumor resection after first-line and salvage chemotherapy.

Results
All patients included had stage III NSGCT. 39 and 11 patients received first-line and salvage chemotherapy, respectively. 45 (90%) patients received retroperitoneal resection first, followed by thoracic surgery. Three patients (6%) underwent thoracic surgery before retroperitoneal surgery and two patients (4%) underwent simultaneous surgery. Overall, the histology of retroperitoneal and thoracic specimens was discordant in 23% of cases. After first-line chemotherapy, of fourteen patients with necrosis in retroperitoneal histology, four patients had vital carcinoma in lung histology. In patients with teratoma in the retroperitoneum, the thoracic findings were concordant in most cases (78%). When teratomatous elements were also present in the orchiectomy specimen, concordance was 100%. After salvage chemotherapy, the discordance rate was 55%.

Conclusion
The data presented in this study underline that retroperitoneal residual masses with necrosis cannot reliably predict histologic findings of thoracic specimens. Patients with teratoma in the retroperitoneum have a high likelihood of teratoma in the thoracic specimen.
Morphotype-specific calcium signaling in human microglia
Authors: Nevelchuk Sofia , Brawek Bianca , Schwarz Niklas , Valiente-Gabioud Ariel , Wuttke Thomas V. , Kovalchuk Yury , Koch Henner , Höllig Anke , Steiner Frederik , Figarella Katherine , Griesbeck Oliver , Garaschuk Olga 
Published: July 2024

Abstract
Background
Key functions of Ca2+ signaling in rodent microglia include monitoring the brain state as well as the surrounding neuronal activity and sensing the danger or damage in their vicinity. Microglial Ca2+ dyshomeostasis is a disease hallmark in many mouse models of neurological disorders but the Ca2+ signal properties of human microglia remain unknown.

Methods
We developed a novel genetically-encoded ratiometric Ca2+ indicator, targeting microglial cells in the freshly resected human tissue, organotypically cultured tissue slices and analyzed in situ ongoing Ca2+ signaling of decades-old microglia dwelling in their native microenvironment.

Results
The data revealed marked compartmentalization of Ca2+ signals, with signal properties differing across the compartments and resident morphotypes. The basal Ca2+ levels were low in ramified and high in ameboid microglia. The fraction of cells with ongoing Ca2+ signaling, the fraction and the amplitude of process Ca2+ signals and the duration of somatic Ca2+ signals decreased when moving from ramified via hypertrophic to ameboid microglia. In contrast, the size of active compartments, the fraction and amplitude of somatic Ca2+ signals and the duration of process Ca2+ signals increased along this pathway.
MAPtools: command-line tools for mapping-by-sequencing and QTL-Seq analysis and visualization
Authors: Martínez-Guardiola César , Parreño Ricardo , Candela Héctor 
Published: July 2024

Abstract
Background
Classical mutagenesis is a powerful tool that has allowed researchers to elucidate the molecular and genetic basis of a plethora of processes in many model species. The integration of these methods with modern massively parallel sequencing techniques, initially in model species but currently also in many crop species, is accelerating the identification of genes underlying a wide range of traits of agronomic interest.

Results
We have developed MAPtools, an open-source Python3 application designed specifically for the analysis of genomic data from bulked segregant analysis experiments, including mapping-by-sequencing (MBS) and quantitative trait locus sequencing (QTL-seq) experiments. We have extensively tested MAPtools using datasets published in recent literature.

Conclusions
MAPtools gives users the flexibility to customize their bioinformatics pipeline with various commands for calculating allele count-based statistics, generating plots to pinpoint candidate regions, and annotating the effects of SNP and indel mutations. While extensively tested with plants, the program is versatile and applicable to any species for which a mapping population can be generated and a sequenced genome is available.

Availability and implementation
MAPtools is available under GPL v3.0 license and documented as a Python3 package at https://github.com/hcandela/MAPtools.
Treatment outcomes of surgery followed by short-course every other day radiotherapy in keloid
Authors: Zhou Wei , Li Bing , Yin Yutian , Zhang Lihua , Zhou Yan , Xu Lin , Zang Jian , Zhao Lina 
Published: July 2024

Abstract
Background
Postoperative radiotherapy can significantly reduce keloid recurrence. However, consensus on the optimal radiotherapy dose and treatment schedule remains elusive. This study aims to evaluate the effectiveness of surgery followed by a short-course of radiotherapy administered every other day for keloid treatment.

Materials/Methods
We conducted a retrospective analysis of 498 patients with keloids treated at our institution between January 2010 and December 2017. All patients underwent electron beam irradiation at a dose of 16 Gy, delivered in four fractions every other day, starting within 24 h post-surgery. The primary endpoint of the study was the local control rate.

Results
A total of 130 (26.5%) keloids recurred after a median follow-up of 68.1months (42.6-129.9 months). The local control rates at 1 year, 3 years and 5 years for all patients were 89.5%, 82.5% and 81%, respectively. The highest recurrence rate was observed in keloids located in the chest region (50.8%), followed by the suprapubic (47.8%), head and neck (38.8%), limbs (33.3%) and ear (14%). Both multivariate and univariate analyses identified the presence of pain and or pruritus as an independently prognostic factor for keloid recurrence (p<0.0001). The local control rates at 1-year, 3-years and 5-years for patients with or without symptom of pain or pruritus were 45% vs. 98.8%, 12.5% vs. 95.9%, and 8.8% vs. 95%, respectively (HR:37.829, 95%CI: 24.385–58.686, p<0.001). In the ear keloid subgroup, the 1-year, 3-year and 5-year local control rates for patients with pruritus were significantly lower than those without pain or pruritus (60.0% vs. 97.9%, 26.7% vs. 94.7%, 26.7% vs. 94.3%, HR:30.209, 95% CI:14.793–61.69, p<0.001). The same results were found in other location(p<0.001). During treatment and follow-up, two patients experienced infections, and one patient developed a cutaneous fibroblastoma.

Conclusion
This study suggests that a combination of surgery followed by short-course, every-other-day radiotherapy can yield satisfactory local control rates for keloids. Pain and or pruritus symptom was an independently prognostic factors for recurrence of keloid. To further validate these results, a prospective randomized controlled trial is recommended.
Consensus-based expert recommendations on the management of MPS IVa and VI in Saudi Arabia
Authors: AlSayed Moeenaldeen , Arafa Dia , Al-Khawajha Huda , Afqi Manal , Al-Sanna’a Nouriya , Sunbul Rawda , Faden Maha 
Published: July 2024

AbstractBackgroundMucopolysaccharidosis type IVa (Morquio A syndrome) and mucopolysaccharidosis type VI (Maroteaux-Lamy syndrome) are rare inherited lysosomal storage diseases associated with significant functional impairment and a wide spectrum of debilitating clinical manifestations. These conditions are thought to have higher-than-average prevalence rates in Saudi Arabia due to high rates of consanguineous marriage in the country. There are several unmet needs associated with the management of these diseases in Saudi Arabia.Main bodyThe aim of this manuscript is to contextualize unmet management needs and provide recommendations to optimize diagnosis, multidisciplinary care delivery, and local data generation in this disease area. An expert panel was assembled comprising seven consultant geneticists from across Saudi Arabia. The Delphi methodology was used to obtain a consensus on statements relating to several aspects of mucopolysaccharidosis types IVa and VI. A consensus was reached for all statements by means of an online, anonymized voting system. The consensus statements pertain to screening and diagnosis, management approaches, including recommendations pertaining to enzyme replacement therapy, and local data generation.ConclusionThe consensus statements presented provide specific recommendations to improve diagnostic and treatment approaches, promote multidisciplinary care and data sharing, and optimize the overall management of these rare inherited diseases in Saudi Arabia.
Plasmacytoid dendritic cells at the forefront of anti-cancer immunity: rewiring strategies for tumor microenvironment remodeling
Authors: Monti Matilde , Ferrari Giorgia , Gazzurelli Luisa , Bugatti Mattia , Facchetti Fabio , Vermi William 
Published: July 2024

AbstractPlasmacytoid dendritic cells (pDCs) are multifaceted immune cells executing various innate immunological functions. Their first line of defence consists in type I interferons (I-IFN) production upon nucleic acids sensing through endosomal Toll-like receptor (TLR) 7- and 9-dependent signalling pathways. Type I IFNs are a class of proinflammatory cytokines that have context-dependent functions on cancer immunosurveillance and immunoediting. In the last few years, different studies have reported that pDCs are also able to sense cytosolic DNA through cGAS–STING (stimulator of interferon genes) pathway eliciting a potent I-IFN production independently of TLR7/9. Human pDCs are also endowed with direct effector functions via the upregulation of TRAIL and production of granzyme B, the latter modulated by cytokines abundant in cancer tissues. pDCs have been detected in a wide variety of human malignant neoplasms, including virus-associated cancers, recruited by chemotactic stimuli. Although the role of pDCs in cancer immune surveillance is still uncompletely understood, their spontaneous activation has been rarely documented; moreover, their presence in the tumor microenvironment (TME) has been associated with a tolerogenic phenotype induced by immunosuppressive cytokines or oncometabolites. Currently tested treatment options can lead to pDCs activation and disruption of the immunosuppressive TME, providing a relevant clinical benefit. On the contrary, the antibody–drug conjugates targeting BDCA-2 on immunosuppressive tumor-associated pDCs (TA-pDCs) could be proposed as novel immunomodulatory therapies to achieve disease control in patients with advance stage hematologic malignancies or solid tumors. This Review integrate recent evidence on the biology of pDCs and their pharmacological modulation, suggesting their relevant role at the forefront of cancer immunity.
Balancing pH and yield: exploring itaconic acid production in Ustilago cynodontis from an economic perspective
Authors: Ernst Philipp , Saur Katharina Maria , Kiefel Robert , Niehoff Paul-Joachim , Weskott Ronja , Büchs Jochen , Jupke Andreas , Wierckx Nick 
Published: July 2024

Abstract
Background
Itaconic acid is a promising bio-based building block for the synthesis of polymers, plastics, fibers and other materials. In recent years, Ustilago cynodontis has emerged as an additional itaconate producing non-conventional yeast, mainly due to its high acid tolerance, which significantly reduces saline waste coproduction during fermentation and downstream processing. As a result, this could likely improve the economic viability of the itaconic acid production process with Ustilaginaceae.

Results
In this study, we characterized a previously engineered itaconate hyper-producing Ustilago cynodontis strain in controlled fed-batch fermentations to determine the minimal and optimal pH for itaconate production. Under optimal fermentation conditions, the hyper-producing strain can achieve the theoretical maximal itaconate yield during the production phase in a fermentation at pH 3.6, but at the expense of considerable base addition. Base consumption is strongly reduced at the pH of 2.8, but at cost of production yield, titer, and rate. A techno-economic analysis based on the entire process demonstrated that savings due to an additional decrease in pH control reagents and saline waste costs cannot compensate the yield loss observed at the highly acidic pH value 2.8.

Conclusions
Overall, this work provides novel data regarding the balancing of yield, titer, and rate in the context of pH, thereby contributing to a better understanding of the itaconic acid production process with Ustilago cynodontis, especially from an economic perspective.
JAK inhibitors attenuate hyperactivation of nonswitched memory B cells in rheumatoid arthritis patients in remission
Authors: Luo Jing , Zhang Jing , Ju Bomiao , Wang Yanhua , Hu Nan , Li Qian , Xu Qianyun , Pu Dan , Hao Zhiming , Huo Yongwei , Lv Xiaohong , He Lan 
Published: July 2024

Abstract
Objective
To investigate the distribution and activation of B-cell subpopulations in rheumatoid arthritis (RA) patients treated with Janus kinase inhibitors (JAKis) and to analyze their correlation with disease remission.

Methods
Peripheral blood samples were collected from 23 adult healthy controls and 58 RA patients, 31 of whom were treated with JAKis and assessed during a 24-month follow-up. The number of peripheral B-cell subpopulations (including naive B cells, nonswitched memory B (NSMB) cells, switched memory B cells, and double-negative B cells), their activation, and phosphorylation of SYK and AKT upon B-cell receptor (BCR) stimulation in each population were analyzed by flow cytometry.

Results
Compared with that in healthy controls, the frequency of NSMB cells was significantly lower in new-onset untreated RA patients. However, expression of CD40, CD80, CD95, CD21low and pAKT significantly increased in these NSMB cells. Additionally, the number of NSMB cells correlated negatively with DAS28-ESR and IgG and IgA levels in these patients; expression of CD80, CD95 and CD21low on NSMB cells correlated positively with DAS28-ESR and IgG and IgA levels. After treatment with JAKis, the serum IgG concentration significantly decreased in RA patients in remission, but CD40, CD95 and pAKT levels in NSMB cells significantly decreased.

Conclusion
RA patients present different B-cell subpopulations, in which the frequency of NSMB cells is negatively associated with disease activity. However, treatment with JAKis can inhibit activation of NSMB cells, restore the balance of kinase phosphorylation, and facilitate disease remission in RA patients.
Applicability of combined high-frequency and contrast-enhanced ultrasound in finger extensor tendon injuries: three case reports
Authors: Wang Wenying , Peng Li , He Lian , Chen Yan , Jiang Mingshan , Luo Xue , Gao Guoqiang 
Published: July 2024

Abstract
Background
By combining high-frequency and contrast-enhanced ultrasound (CEUS), the position of the severed end of a finger extensor tendon injury and the injury classification can be determined as part of a comprehensive preoperative evaluation in clinical practice. However, there have been no reports of high-frequency ultrasound combined with CEUS for the preoperative diagnosis of human finger extensor tendon injury.

Cases presentation
One case of complete rupture of the extensor tendon was diagnosed by ultrasound, which was completely consistent with the surgery; one case of incomplete rupture was ultimately confirmed clinically; and one case of distal phalangeal bone base avulsion fracture with tendon contusion and missed diagnosis on the first radiographic examination was confirmed by follow-up radiographic examination.

Conclusions
Different types of finger extensor tendon injuries exhibit distinctive contrast-enhanced ultrasonography findings. Combined high-frequency and contrast-enhanced ultrasound can accurately locate the position of the severed end of the finger extensor tendon injury before surgery while observing the contrast agent filling area to clarify injury classification, providing a reliable imaging basis for clinical practice and ultimately developing personalized diagnosis and treatment plans for patients to ensure minimal trauma and pain, as well as optimal treatment effects.
Assessment of the intensity and attractiveness of physical exercise while playing table tennis in an immersive virtual environment depending on the game mode
Authors: Polechoński Jacek 
Published: July 2024

Abstract
Background
It appears that active video games (AVGs) and training apps that allow for physical activity (PA) in immersive virtual reality (VR) may be useful for sports, health-enhancing PA, and physical education (PE). Therefore, research is needed to identify their potential.

Objective
The study aimed to evaluate the intensity and attractiveness of exercise during table tennis (TT) training in VR in arcade and simulation modes and to assess the potential for using such exercises in health-enhancing PA, sport, and PE.

Methods
The research used the Racket Fury: Table Tennis VR. Exercise intensity during TT training in VR was evaluated by heart rate (HR) monitoring and rating of perceived exertion (RPE 6–20). The effectiveness of short-term TT training in VR was estimated based on the user’s performance in playing against an opponent with artificial intelligence (AI), satisfaction with playing TT was measured using the Physical Activity Enjoyment Scale (PACES), and the potential usefulness of the tested app in PA, sport, and PE was assessed based on a questionnaire for participating PE teachers (30 participants).

Results
PA intensity during TT training in VR expressed as a percentage of maximum heart rate (HRmax) was moderate but was significantly (p < 0.001; d=-0.830) higher in the easier arcade mode (69.50 ± 12.58%HRmax) than in the simulation mode (64.10 ± 9.67%HRmax). Despite the greater fatigue of respondents, user satisfaction was significantly higher in arcade mode. Users’ performance when playing with AI was significantly better after 20 min of training in VR than before training. PE teachers recognize the great potential of the app.

Conclusions
The application tested is characterized by a beneficial PA intensity, with its level depending on the game mode. Facilitating strokes during a game of virtual TT promotes increased intensity of exercise and increased enjoyment of the PA. Short-term TT training in VR improves playing skills in a virtual environment. PE teachers spoke highly of the app and recognized the potential for using VR technology in PA, sports, and school PE.
Thermographic analysis of perforations in polyurethane blocks performed with experimental conical drill bit in comparison to conventional orthopedic drill bit: a preliminary study
Authors: Rovaris Inácio Bernhardt , de Carvalho Anderson Luiz , Silva Gabriel Aardewijn , Gerardi Daniel Guimarães , Alievi Marcelo Meller 
Published: July 2024

Abstract
Objective
Conical orthopedic drill bits may have the potential to improve the stabilization of orthopedic screws. During perforations, heat energy is released, and elevated temperatures could be related to thermal osteonecrosis. This study was designed to evaluate the thermal behavior of an experimental conical drill bit, when compared to the conventional cylindrical drill, using polyurethane blocks perforations.

Results
The sample was divided into two groups, according to the method of drilling, including 25 polyurethane blocks in each: In Group 1, perforations were performed with a conventional orthopedic cylindrical drill; while in Group 2, an experimental conical drill was used. No statistically significant difference was observed in relation to the maximum temperature (MT) during the entire drilling in the groups, however the perforation time (PT) was slightly longer in Group 2. Each drill bit perforated five times and number of perforations was not correlated with a temperature increase, when evaluated universally or isolated by groups. The PT had no correlation with an increase in temperature when evaluating the perforations universally (n = 50) and in Group 1 alone; however, Group 2 showed an inversely proportional correlation for these variables, indicating that, for the conical drill bit, drillings with longer PT had lower MT.
Health markers, depressive symptoms, and community deprivation in a type 2 diabetes multidisciplinary care clinic for youth
Authors: Bejarano Carolina M. , Ley Sanita , Krishnan Nisha , Orkin Sarah , Crimmins Nancy A. , Schaaf Lisa , Shah Amy S. 
Published: July 2024

Abstract
Introduction
Type 2 diabetes disproportionately affects non-Hispanic/Latino Black and Hispanic/Latino youth. The purpose of this study was to examine whether differences in metabolic risk factors and depressive symptoms exist by race/ethnicity and socioeconomic deprivation and whether these impact clinic attendance and health markers over 1 year in a multidisciplinary type 2 diabetes clinic for youth.

Methods
This study was a retrospective chart review of 54 youth with type 2 diabetes who had both an initial and follow-up visit. Demographic information, metabolic health markers [body mass index (BMI), hemoglobin A1C, liver enzymes, lipid panel, and urine microalbumin], depressive symptoms, and clinic attendance data were obtained from the medical record. Patient address was geocoded to the census tract level to calculate community socioeconomic deprivation.

Results
Liver enzymes (ALT and AST) were significantly higher in patients identifying as Hispanic/Latino (ALT M = 97.0 ± 40.6, AST M = 53.6 ± 21.4) and lowest in patients identifying as non-Hispanic/Latino Black (ALT M = 23.1 ± 11.3, F = 10.6 p < .001; AST M = 23.1 ± 11.4, F = 8.1; p < .001) at initial visit. From initial visit to follow-up, there were significant improvements in ALT (F = 13.43, p < .001), AST (F = 6.58, p < .05), and BMIz (F = 18.39, p < .001). Patients identifying as Black or Hispanic showed an increase in depressive symptoms over time, while patients identifying as non-Hispanic White showed a decrease (F = 11.08; p < .05). Unexpectedly, patients living in areas with higher socioeconomic deprivation showed a decrease in hemoglobin A1C over time, while patients living in lower socioeconomic deprivation showed an increase (F = 5.15, p < .05).

Conclusions
Differences exist in metabolic health parameters by race/ethnicity and by socioeconomic deprivation. Multidisciplinary care for youth with type 2 diabetes needs to consider and work to address the systems of inequity experienced by patients that drive disparities in health outcomes.