bluuebunny/crossref_metadata_2025_split huggingface dataset:
Risk Assessment of Industrial Microbes Using a Terrestrial Mesocosm Platform
Authors: Arnolds Kathleen L. , Higgins Riley C. , Crandall Jennifer , Li Gabriella , Linger Jeffrey G. , Guarnieri Michael T. 
Published: December 2023

AbstractIndustrial microbes and bio-derived products have emerged as an integral component of the bioeconomy, with an array of agricultural, bioenergy, and biomedical applications. However, the rapid development of microbial biotechnology raises concerns related to environmental escape of laboratory microbes, detection and tracking thereof, and resultant impact upon native ecosystems. Indeed, though wild-type and genetically modified microbes are actively deployed in industrial bioprocesses, an understanding of microbial interactivity and impact upon the environment is severely lacking. In particular, the persistence and sustained ecosystem impact of industrial microbes following laboratory release or unintentional laboratory escape remains largely unexplored. Herein, we investigate the applicability of soil-sorghum mesocosms for the ecological risk assessment of the industrial microbe, Saccharomyces cerevisiae. We developed and applied a suite of diagnostic and bioinformatic analyses, including digital droplet PCR, microscopy, and phylogenomic analyses to assess the impacts of a terrestrial ecosystem perturbation event over a 30-day time course. The platform enables reproducible, high-sensitivity tracking of S. cerevisiae in a complex soil microbiome and analysis of the impact upon abiotic soil characteristics and soil microbiome population dynamics and diversity. The resultant data indicate that even though S. cerevisiae is relatively short-lived in the soil, a single perturbation event can have sustained impact upon mesocosm soil composition and underlying microbial populations in our system, underscoring the necessity for more comprehensive risk assessment and development of mitigation and biocontainment strategies in industrial bioprocesses.
The overlooked bacterial pandemic
Authors: Moriel Danilo Gomes , Piccioli Diego , Raso Maria Michelina , Pizza Mariagrazia 
Published: December 2023

AbstractThe COVID-19 pandemic had a significant economic and health impact worldwide. It also reinforced the misperception that only viruses can pose a threat to human existence, overlooking that bacteria (e.g., plague and cholera) have severely haunted and shaped the course of human civilization. While the world is preparing for the next viral pandemic, it is again overlooking a silent one: antimicrobial resistance (AMR). This review proposes to show the impact of bacterial infections on civilization to remind the pandemic potential. The work will also discuss a few examples of how bacteria can mutate risking global spread and devastating outcomes, the effect on the global burden, and the prophylactic and therapeutic measures. Indeed, AMR is dramatically increasing and if the trend is not reversed, it has the potential to quickly turn into the most important health problem worldwide.
A formative journal for a formative career: a personal recollection of how JCPA has inspired and guided my research life
Authors: Warrant Eric J. 
Published: December 2023

AbstractA fateful decision as a 15-year-old high school student, and good advice from a distinguished professor of zoology, were the catalysts that not only decided my entire career but also led me to the Journal of Comparative Physiology A, and to the myriad biological wonders that were held within its covers. In my celebration of JCPA, I look back on the formative years of my career in Australia, and the crucial role that the journal played in shaping my emerging research interests, and ultimately my entire life.
VARC-3 defined outcome of valve-in-valve transcatheter aortic valve implantation in stentless compared with stented aortic bioprostheses
Authors: Steul Jean-Honoré , Abdel-Wahab Mohamed , Stankowski Tomasz , Haussig Stephan , Woitek Felix J. , Gasior Tomasz , Crusius Lisa , Knorr Luise , Müller Felicitas V. , Fritzsche Dirk , Kiefer Philipp , Kappert Utz , Holzhey David , Linke Axel , Mangner Norman 
Published: December 2023

Abstract
Background
Valve-in-valve (ViV) transcatheter aortic valve implantation (TAVI) is a viable alternative to redo surgery in selected patients with bioprosthetic valve dysfunction. Most ViV-TAVI procedures have been performed in stented bioprosthetic valves (ST); stentless bioprostheses (SL) lack fluoroscopic markers and could be more challenging for ViV-TAVI. Data on more recent patients applying Valve Academic Research Consortium (VARC)-3 defined outcomes are scarce. We compared patient characteristics, procedural outcomes, and 5-year mortality of patients with SL versus ST aortic bioprosthetic valve failure undergoing ViV-TAVI.

Methods
Patients undergoing ViV-TAVI between 2007 and 2022 (52.5% of cases after 2015) at 3 German centers were included in this analysis. The co-primary outcome measures were technical success, device success, and early safety defined by VARC-3. Mortality was assessed up to 5 years.

Results
Overall, 43 (11.8%) SL and 313 (88.2%) ST ViV-TAVI were included. Patients were comparable with regard to age, sex, clinically relevant baseline comorbidities, and surgical risk.
Technical success (SL: 83.7% versus ST: 79.9%, p = 0.552), device success (SL: 67.4% versus ST: 54.3%, p = 0.105), and early safety (SL: 74.4% versus ST: 66.5%, p = 0.296) were comparable between groups. The 30-day mortality (SL: 7.0% versus ST: 2.6%, p = 0.136) and 5-year mortality rates (SL: 23.3% versus ST: 24.6%, p = 0.874) were not significantly different between groups.

Conclusion
SL and ST ViV-TAVI led to comparable short-term outcomes according to VARC-3- defined endpoints and similar mortality rates up to 5 years of follow-up.

Graphical abstract
“De novo replication repair deficient glioblastoma, IDH-wildtype” is a distinct glioblastoma subtype in adults that may benefit from immune checkpoint blockade
Authors: Hadad Sara , Gupta Rohit , Oberheim Bush Nancy Ann , Taylor Jennie W. , Villanueva-Meyer Javier E. , Young Jacob S. , Wu Jasper , Ravindranathan Ajay , Zhang Yalan , Warrier Gayathri , McCoy Lucie , Shai Anny , Pekmezci Melike , Perry Arie , Bollen Andrew W. , Phillips Joanna J. , Braunstein Steve E. , Raleigh David R. , Theodosopoulos Philip , Aghi Manish K. , Chang Edward F. , Hervey-Jumper Shawn L. , Costello Joseph F. , de Groot John , Butowski Nicholas A. , Clarke Jennifer L. , Chang Susan M. , Berger Mitchel S. , Molinaro Annette M. , Solomon David A. 
Published: December 2023

AbstractGlioblastoma is a clinically and molecularly heterogeneous disease, and new predictive biomarkers are needed to identify those patients most likely to respond to specific treatments. Through prospective genomic profiling of 459 consecutive primary treatment-naïve IDH-wildtype glioblastomas in adults, we identified a unique subgroup (2%, 9/459) defined by somatic hypermutation and DNA replication repair deficiency due to biallelic inactivation of a canonical mismatch repair gene. The deleterious mutations in mismatch repair genes were often present in the germline in the heterozygous state with somatic inactivation of the remaining allele, consistent with glioblastomas arising due to underlying Lynch syndrome. A subset of tumors had accompanying proofreading domain mutations in the DNA polymerase POLE and resultant “ultrahypermutation”. The median age at diagnosis was 50 years (range 27–78), compared with 63 years for the other 450 patients with conventional glioblastoma (p < 0.01). All tumors had histologic features of the giant cell variant of glioblastoma. They lacked EGFR amplification, lacked combined trisomy of chromosome 7 plus monosomy of chromosome 10, and only rarely had TERT promoter mutation or CDKN2A homozygous deletion, which are hallmarks of conventional IDH-wildtype glioblastoma. Instead, they harbored frequent inactivating mutations in TP53, NF1, PTEN, ATRX, and SETD2 and recurrent activating mutations in PDGFRA. DNA methylation profiling revealed they did not align with known reference adult glioblastoma methylation classes, but instead had unique globally hypomethylated epigenomes and mostly classified as “Diffuse pediatric-type high grade glioma, RTK1 subtype, subclass A”. Five patients were treated with immune checkpoint blockade, four of whom survived greater than 3 years. The median overall survival was 36.8 months, compared to 15.5 months for the other 450 patients (p < 0.001). We conclude that “De novo replication repair deficient glioblastoma, IDH-wildtype” represents a biologically distinct subtype in the adult population that may benefit from prospective identification and treatment with immune checkpoint blockade.
The use of colposcopy for triage in HPV-positive women aged 65 years and older
Authors: Kuenkel E. , Jaeger A. , Bohlmann I. , Bergauer F. , Kuehler-Obbarius C. , Prieske K. , Maass-Poppenhusen K. , Schmalfeldt B. , Woelber L. 
Published: December 2023

Abstract
Purpose
Persistent high-risk HPV infection is associated with an elevated risk for prevalent CIN II + despite normal cytology (NILM). Our study aims to evaluate the clinical relevance of a persistent high-risk HPV infection without cytologic changes in women aged ≥ 65 and to determine the role of colposcopy for triage in these cases.

Methods
211 patients aged ≥ 65 with persistent HPV infection and normal cytology (NILM) who presented for colposcopy at five certified centers between January 2021 and April 2022 were included in the study. Colposcopic findings, HPV subtypes, when available, histology and p16/Ki67 staining were assessed as well as individual risk factors such as smoking and previous HPV-related surgery.

Results
87.7% (185/211) of the included women had a type 3 transformation zone. In 83.4% (176/211), a biopsy was taken [thereof 163 endocervical curettages (ECC)]. In 35/211 women (16.6%), sampling was not possible during colposcopy due to an inaccessible cervix, pain during examination or obliteration of the cervical canal. Out of these, 6 women received a diagnostic excision. CIN II + was detected in 10.6% of all histologies (excisional or biopsy) (20/182). 50% of the women with a CIN II + where HPV 16 positive. Taking only the women diagnosed with CIN III or AIS into account, (n = 12) 75% were HPV 16 positive. Interestingly, 80% of the women with CIN II + had an abnormal cytology when repeatedly taken during colposcopy, vice versa an endocervical lesion was diagnosed in 53% of women with abnormal repeat cytology (27/51).

Conclusion
The prevalence of CIN II + in women is ≥ 65 with persistent hr HPV infection but NILM cytology is similar to that in younger women. However, more than 85% of the women have a type 3 transformation zone. Colposcopy is, therefore, not helpful to diagnose the women who need treatment in this age group.
Expanding clinical profiles and prognostic markers in stiff person syndrome spectrum disorders
Authors: Wang Yujie , Hu Chen , Aljarallah Salman , Reyes Mantilla Maria , Mukharesh Loulwah , Simpson Alexandra , Roy Shuvro , Harrison Kimystian , Shoemaker Thomas , Comisac Michael , Balshi Alexandra , Obando Danielle , Maldonado Daniela A. Pimentel , Koshorek Jacqueline , Snoops Sarah , Fitzgerald Kathryn C. , Newsome Scott D. 
Published: December 2023

Abstract
Objective
To describe the clinical features of a cohort of individuals with stiff person syndrome spectrum disorders (SPSD) and identify potential early predictors of future disability.

Background
There is a need to better understand the full spectrum of clinical and paraclinical features and long-term impact of SPSD.

Design/Methods
Observational study from 1997 to 2022 at Johns Hopkins. Clinical phenotypes included classic SPS, partial SPS (limb or trunk limited), SPS-plus (classic features plus cerebellar/brainstem involvement), and progressive encephalomyelitis with rigidity and myoclonus (PERM). Outcome measures were modified Rankin scale (mRS) and use of assistive device for ambulation. Multivariate logistic regression was used to assess significant predictors of outcomes.

Results
Cohort included 227 individuals with SPSD with mean follow-up of 10 years; 154 classic, 48 SPS-plus, 16 PERM, and 9 partial. Mean age at symptom onset was 42.9 ± 14.1 years, majority were white (69.2%) and female (75.8%). Median time to diagnosis was 36.2 months (longest for SPS-plus and PERM) and 61.2% were initially misdiagnosed. Most had systemic co-morbidities and required assistive devices for ambulation. Female sex (OR 2.08; CI 1.06–4.11) and initial brainstem/cerebellar involvement (OR 4.41; CI 1.63–14.33) predicted worse outcome by mRS. Older age at symptom onset (OR 1.04; CI 1.01–1.06), female sex (OR 1.99; CI 1.01–4.01), Black race (OR 4.14; CI 1.79–10.63), and initial brainstem/cerebellar involvement (OR 2.44; CI 1.04–7.19) predicted worse outcome by use of assistive device. Early implementation of immunotherapy was associated with better outcomes by either mRS (OR 0.45; CI 0.22–0.92) or use of assistive device (OR 0.79; CI 0.66–0.94).

Conclusions
We present the expanding phenotypic variability of this rare spectrum of disorders and highlight potential predictors of future disability.
Does the expression of granzyme B participate in inflammation, fibrosis, and fertility of hydatid cysts?
Authors: Sweed Dina , Mohamady Mohamed , Gouda Marwa A. , Fayed Yahya , Saied Sara A. , Elhamed Sara M. Abd 
Published: December 2023

AbstractEchinococcus granulosus (sensu lato), a cestode that is endemic in Egypt, causes cystic echinococcosis (CE), a significant but neglected zoonotic disease that is prevalent throughout the world. Infected hydatid cysts are classified as fertile or non-fertile based on the presence of protoscoleces; nevertheless, the mechanism of non-fertile CE cysts remains unknown. The study aimed to assess whether granzyme B (GrB) expression and CD4 + /CD8 + could be related to the induction of non-fertile CE cysts. A total of fifty-eight individuals diagnosed with visceral hydatid cysts were selected, and they were further divided according to cyst fertility into fertile and non-fertile. Immunohistochemistry for CD4, CD8, and GrB was done. According to the results, hydatid cysts are common in adults and have no gender preference. The same clinical and laboratory data were shared by patients with fertile and non-fertile cysts (p = 0.186). GrB expression was not impacted by the fibrous deposition inside the hydatid cyst wall (p = 0.85); however, GrB was significantly correlated with the inflammatory density (p = 0.005). GrB expression was also found to be significantly higher in non-fertile cysts (p = 0.04). GrB expression is positively correlated with CD4 and CD8 expression. In conclusion, the expression of GrB in hydatid cysts may exacerbate the inflammatory response and impede cyst fertility while not affecting the fibrous deposition in the cyst wall.
SleepSmart: an IoT-enabled continual learning algorithm for intelligent sleep enhancement
Authors: Gamel Samah A. , Talaat Fatma M. 
Published: December 2023

AbstractSleep is an essential physiological process that is crucial for human health and well-being. However, with the rise of technology and increasing work demands, people are experiencing more and more disrupted sleep patterns. Poor sleep quality and quantity can lead to a wide range of negative health outcomes, including obesity, diabetes, and cardiovascular disease. This research paper proposes a smart sleeping enhancement system, named SleepSmart, based on the Internet of Things (IoT) and continual learning using bio-signals. The proposed system utilizes wearable biosensors to collect physiological data during sleep, which is then processed and analyzed by an IoT platform to provide personalized recommendations for sleep optimization. Continual learning techniques are employed to improve the accuracy of the system's recommendations over time. A pilot study with human subjects was conducted to evaluate the system's performance, and the results show that SleepSmart can significantly improve sleep quality and reduce sleep disturbance. The proposed system has the potential to provide a practical solution for sleep-related issues and enhance overall health and well-being. With the increasing prevalence of sleep problems, SleepSmart can be an effective tool for individuals to monitor and improve their sleep quality.
Regional variations and deprivation are linked to poorer access to laparoscopic and robotic colorectal surgery: a national study in England
Authors: Morton A. J. , Simpson A. , Humes D. J. 
Published: December 2023

Abstract
Background
Laparoscopic and now robotic colorectal surgery has rapidly increased in prevalence; however, little is known about how uptake varies by region and sociodemographics. The aim of this study was to quantify the uptake of minimally invasive colorectal surgery (MIS) over time and variations by region, sociodemographics and ethnicity.

Methods
Retrospective analysis of routinely collected healthcare data (Clinical Practice Research Datalink linked to Hospital Episode Statistics) for all adults having elective colorectal resectional surgery in England from 1 January 2006 to 31 March 2020. Sociodemographics between modalities were compared and the association between sociodemographic factors, region and year on MIS was compared in multivariate logistic regression analysis.

Results
A total of 93,735 patients were included: 52,098 open, 40,622 laparoscopic and 1015 robotic cases. Laparoscopic surgery surpassed open in 2015 but has plateaued; robotic surgery has rapidly increased since 2017, representing 3.2% of cases in 2019. Absolute differences up to 20% in MIS exist between regions, OR 1.77 (95% CI 1.68–1.86) in South Central and OR 0.75 (95% CI 0.72–0.79) in the North West compared to the largest region (West Midlands). MIS was less common in the most compared to least deprived (14.6% of MIS in the most deprived, 24.8% in the least, OR 0.85 95% CI 0.81–0.89), with a greater difference in robotic surgery (13.4% vs 30.5% respectively). Female gender, younger age, less comorbidity, Asian or ‘Other/Mixed’ ethnicity and cancer indication were all associated with increased MIS.

Conclusions
MIS has increased over time, with significant regional and socioeconomic variations. With rapid increases in robotic surgery, national strategies for procurement, implementation, equitable distribution and training must be created to avoid worsening health inequalities.
Screening for Circulating Inflammatory Proteins Does Not Reveal Plasma Biomarkers of Constant Tinnitus
Authors: Cederroth Christopher R. , Hong Mun-Gwan , Freydin Maxim B. , Edvall Niklas K. , Trpchevska Natalia , Jarach Carlotta , Schlee Winfried , Schwenk Jochen M. , Lopez-Escamez Jose-Antonio , Gallus Silvano , Canlon Barbara , Bulla Jan , Williams Frances M. K. 
Published: December 2023

Abstract
Background and Objective
Tinnitus would benefit from an objective biomarker. The goal of this study is to identify plasma biomarkers of constant and chronic tinnitus among selected circulating inflammatory proteins.

Methods
A case–control retrospective study on 548 cases with constant tinnitus and 548 matched controls from the Swedish Tinnitus Outreach Project (STOP), whose plasma samples were examined using Olink’s Inflammatory panel. Replication and meta-analysis were performed using the same method on samples from the TwinsUK cohort. Participants from LifeGene, whose blood was collected in Stockholm and Umeå, were recruited to STOP for a tinnitus subtyping study. An age and sex matching was performed at the individual level. TwinsUK participants (n = 928) were selected based on self-reported tinnitus status over 2 to 10 years. Primary outcomes include normalized levels for 96 circulating proteins, which were used as an index test. No reference standard was available in this study.

Results
After adjustment for age, sex, BMI, smoking, hearing loss, and laboratory site, the top proteins identified were FGF-21, MCP4, GDNF, CXCL9, and MCP-1; however, these were no longer statistically significant after correction for multiple testing. Stratification by sex did not yield any significant associations. Similarly, associations with hearing loss or other tinnitus-related comorbidities such as stress, anxiety, depression, hyperacusis, temporomandibular joint disorders, and headache did not yield any significant associations. Analysis in the TwinsUK failed in replicating the top candidates. Meta-analysis of STOP and TwinsUK did not reveal any significant association. Using elastic net regularization, models exhibited poor predictive capacity tinnitus based on inflammatory markers [sensitivity = 0.52 (95% CI 0.47–0.57), specificity = 0.53 (0.48–0.58), positive predictive value = 0.52 (0.47–0.56), negative predictive values = 0.53 (0.49–0.58), and AUC = 0.53 (0.49–0.56)].

Discussion
Our results did not identify significant associations of the selected inflammatory proteins with constant tinnitus. Future studies examining longitudinal relations among those with more severe tinnitus and using more recent expanded proteomics platforms and sampling of cerebrospinal fluid could increase the likelihood of identifying relevant molecular biomarkers.
From a heavy metal perspective, is macroalgal biomass from Madeira Archipelago and Gran Canaria Island of eastern Atlantic safe for the development of blue bioeconomy products?
Authors: Nunes Nuno , Ferraz Sónia , Venuleo Marianna , Barros Ana I. R. N. A. , de Carvalho Miguel A. A. Pinheiro 
Published: December 2023

AbstractMacroalgae are considered a valuable source of several compounds with nutritional, nutraceutical, cosmeceutical, and pharmaceutical applications. They are also used for crop fertilization and biofortification by introducing important minerals into the soil essential for crop productivity. At the same time, however, they are known bio-accumulators of some heavy metals. In this work, we assessed the content of 7 minerals considered as heavy metals in 25 macroalgae samples, comprising 4 greens, 9 reds and 12 browns, from Madeira Archipelago, Portugal, for their potential use as blue bioeconomy products. These heavy metals included zinc (Zn) with concentrations that ranged from 1.95 – 242.65 mg kg−1 dw, nickel (Ni, 0.6 – 34.78 mg kg−1 dw), copper (Cu, 0.42 – 7.98 mg kg−1 dw), chromium (Cr, 0.47 – 45.74 mg kg−1 dw), cadmium (Cd, 0.1 – 2.58 mg kg−1 dw), lead (Pb, 0.05 – 2.79 mg kg−1 dw) and mercury (Hg, 0.03 – 8.49 µg kg−1 dw). We also analysed 22 samples of beach-cast macroalgae from Gran Canaria Island, Spain, collected from November 2016 to November 2019. The same heavy metals were assessed with their concentrations that ranged as follows: Zn (11.41 – 42.20 mg kg−1 dw), Ni (3.17 – 17.78 mg kg−1 dw), Cu (1.85 – 4.20 mg kg−1 dw), Cr (6.08 – 37.98 mg kg−1 dw), Cd (0.02 – 0.11 g kg−1 dw), Pb (0.16 –5.42 mg kg−1 dw) and Hg (3.59 – 31.00 µg kg−1 dw). These concentrations are all within the normal ranges reported in earlier studies in low industrialized areas, except for the brown algae Gongolaria abies-marina and Sargassum vulgare with high mean (± SD) Cd concentration (1.91 ± 0.36 and 1.75 ± 0.07 g kg−1 dw respectively). Our results suggest that most of the biomass prospected in these localities covered in the present study would be a viable source of materials for the development of a blue economy industry with emerging products following the European Union directives.
A NOTE ON THE POLAR DECOMPOSITION IN METRIC SPACES
Authors: Avetisyan Zhirayr , Ruzhansky Michael 
Published: December 2023

Abstract
The analogue of polar coordinates in the Euclidean space, a polar decomposition in a metric space, if well-defined, can be very useful in dealing with integrals with respect to a sufficiently regular measure. In this note we handle the technical details associated with such polar decompositions.

Supplementary Information
The online version contains the Armenian language version of the article available at https://doi.org/10.1007/s10958-023-06674-w.