bluuebunny/crossref_metadata_2025_split huggingface dataset:
A germline-specific role for unconventional components of the γ-tubulin complex in Caenorhabditis elegans
Authors: Haruta Nami , Sumiyoshi Eisuke , Honda Yu , Terasawa Masahiro , Uchiyama Chihiro , Toya Mika , Kubota Yukihiko , Sugimoto Asako 
Published: June 2023

ABSTRACT
The γ-tubulin complex (γTuC) is a widely conserved microtubule nucleator, but some of its components, namely GCP4, GCP5 and GCP6 (also known as TUBGCP4, TUBGCP5 and TUBGCP6, respectively), have not been detected in Caenorhabditis elegans. Here, we identified two γTuC-associated proteins in C. elegans, GTAP-1 and GTAP-2, for which apparent orthologs were detected only in the genus Caenorhabditis. GTAP-1 and GTAP-2 were found to localize at centrosomes and the plasma membrane of the germline, and their centrosomal localization was interdependent. In early C. elegans embryos, whereas the conserved γTuC component MZT-1 (also known as MOZART1 and MZT1) was essential for the localization of centrosomal γ-tubulin, depletion of GTAP-1 and/or GTAP-2 caused up to 50% reduction of centrosomal γ-tubulin and precocious disassembly of spindle poles during mitotic telophase. In the adult germline, GTAP-1 and GTAP-2 contributed to efficient recruitment of the γTuC to the plasma membrane. Depletion of GTAP-1, but not of GTAP-2, severely disrupted both the microtubule array and the honeycomb-like structure of the adult germline. We propose that GTAP-1 and GTAP-2 are unconventional components of the γTuC that contribute to the organization of both centrosomal and non-centrosomal microtubules by targeting the γTuC to specific subcellular sites in a tissue-specific manner.
Ectotherm heat tolerance and the microbiome: current understanding, future directions and potential applications
Authors: Fontaine Samantha S. , Kohl Kevin D. 
Published: June 2023

ABSTRACT
Climate change and increasing global temperatures are a leading threat to ectothermic animals worldwide. Ectotherm persistence under climate change will depend on a combination of host and environmental factors; recently it has become clear that host-associated microbial communities contribute significantly to the response of ectotherms to environmental warming. However, several unanswered questions about these relationships remain before accurate predictions can be made regarding the microbiome's influence on host ecology and evolution under climate warming. In this Commentary, we provide a brief background of what is currently known about the influence of the microbiome on heat tolerance in both invertebrate and vertebrate ectothermic animals, and the mechanisms behind these effects. We then outline what we feel are important priorities for future work in the field, and how these goals could be accomplished. We specifically highlight a need for more diversity in study systems, especially through increasing representation of vertebrate hosts and hosts across a variety of life-history traits and habitats, as well as a greater understanding of how these relationships manifest in field settings. Lastly, we discuss the implications of microbiome-mediated heat tolerance for animal conservation under climate change and the possibility of ‘bioaugmentation’ approaches to bolster host heat tolerance in vulnerable populations.
Understanding the high electronic quantum similarity of a series of ligands used as inhibitors of the SARS-CoV-2 virus by molecular mechanics and density functional theory approaches
Authors: Morales-Bayuelo Alejandro , Sánchez-Márquez Jesús 
Published: June 2023

Background: A coronavirus identified in 2019, SARS-CoV-2, has caused a pandemic of respiratory illness, called COVID-19. Most people with COVID-19 experience mild to moderate symptoms and recover without the need for special treatments. The SARS‑CoV‑2 RNA‑dependent RNA polymerase (RdRp) plays a crucial role in the viral life cycle. The active site of the RdRp is a very accessible region, so targeting this region to study the inhibition of viral replication may be an effective therapeutic approach. For this reason, this study has selected and analysed a series of ligands used as SARS-CoV-2 virus inhibitors, namely: Darunavir (Daru), Dexamethasona (Dexame), Dolutegravir (Dolu), Fosamprenavir (Fosam), Ganciclovir (Gan), Insoine (Inso), Lopinavir (Lop), Ritonavir (Rito) and Tipranavir (Tipra). Methods: These ligands were analyzed using molecular docking, molecular quantum similarity using four similarity indices like overlap, Coulomb and their Euclidean distances. On the other hand, these outcomes were supported with chemical reactivity indices defined within a conceptual density functional theory framework. Results: The results show the conformations with the highest root-mean-square deviation (RMSD), have π-π stacking interaction with residue LYS621, ARG555 and ASP623, CYS622, ASP760, among others. In the molecular quantum similarity, the highest indices have been obtained in the electronic similarity in comparison with the structural similarity. Conclusions: These studies allow the identification of the main stabilizing interactions using the crystal structure of SARS‑CoV‑2 RNA‑dependent RNA polymerase. In this order of ideas, this study provides new insights into these ligands that can be used in the design of new COVID-19 treatments. The studies allowed us to find an explanation supported in the Density Functional Theory about the chemical reactivity and the stabilization in the active site of the ligands.
Automated news in practice: a cross-national ANT case study
Authors: Danzon-Chambaud Samuel 
Published: June 2023

Background:This article provides a comprehensive picture of automated news’ usage—understood here as the auto-generation of journalistic text through software and algorithms, with no human intervention in-between except for the initial programming at 18 news organisations in Europe, North America and Australia, following a strategic sample inspired by Hallin and Mancini’s (2004) media system typology.Methods:To describe the many ways it is implemented, I rely on Actor-network theory (ANT) so as to distinguish situations where somethingmoreis added to automated news systems from those where initial intent is kept and where the software does what it is supposed to do. Semi-structured interviews with editorial staff, executives and technologists were conducted remotely and elements of a netnography were also carried out.Results:Overall, my findings show that the main transformations—ortranslations—of automated news systems deal with alternate data sources (e.g., news organisations’ internal feeds, crowdsourced material), new affordances that are specifically built for journalists (e.g., in-house self-editing tools, notification streams) and output other than text (e.g., automated audio summaries for voice assistants). Conclusions: Although these changes lead to greater journalistic professionalisation, they could also make news organisations become too dependent on Big Tech companies for data acquisition and dissemination of automated news products, thus making platforms gain the upper hand in future developments of these systems.
Benders Adaptive-Cuts Method for Two-Stage Stochastic Programs
Authors: Ramírez-Pico Cristian , Ljubić Ivana , Moreno Eduardo 
Published: June 2023

Benders decomposition is one of the most applied methods to solve two-stage stochastic problems (TSSP) with a large number of scenarios. The main idea behind the Benders decomposition is to solve a large problem by replacing the values of the second-stage subproblems with individual variables and progressively forcing those variables to reach the optimal value of the subproblems, dynamically inserting additional valid constraints, known as Benders cuts. Most traditional implementations add a cut for each scenario (multicut) or a single cut that includes all scenarios. In this paper, we present a novel Benders adaptive-cuts method, where the Benders cuts are aggregated according to a partition of the scenarios, which is dynamically refined using the linear program-dual information of the subproblems. This scenario aggregation/disaggregation is based on the Generalized Adaptive Partitioning Method (GAPM), which has been successfully applied to TSSPs. We formalize this hybridization of Benders decomposition and the GAPM by providing sufficient conditions under which an optimal solution of the deterministic equivalent can be obtained in a finite number of iterations. Our new method can be interpreted as a compromise between the Benders single-cuts and multicuts methods, drawing on the advantages of both sides, by rendering the initial iterations faster (as for the single-cuts Benders) and ensuring the overall faster convergence (as for the multicuts Benders). Computational experiments on three TSSPs [the Stochastic Electricity Planning, Stochastic Multi-Commodity Flow, and conditional value-at-risk (CVaR) Facility Location] validate these statements, showing that the new method outperforms the other implementations of Benders methods, as well as other standard methods for solving TSSPs, in particular when the number of scenarios is very large. Moreover, our study demonstrates that the method is not only effective for the risk-neutral decision makers, but also that it can be used in combination with the risk-averse CVaR objective. Funding: Financial support from Agencia Nacional de Investigación y Desarrollo - Chile [FONDECYT 1200809] and STIC-Amsud [STIC19007] is gratefully acknowledged.
Image restoration algorithm for terahertz FMCW radar imaging
Authors: Hu Weidong , Xu Zhihao , Jiang Huanyu , Liu Qingguo , Yao Zhiyu , Tan Zhen , Ligthart Leo P. 
Published: June 2023

The terahertz frequency modulation continuous-wave (THz FMCW) imaging technology has been widely used in non-destructive testing applications. However, THz FMCW real-aperture radar usually has a small depth of field and poor lateral resolution, thus restricting the high-precision imaging application. This paper proposes a 150–220 GHz FMCW Bessel beam imaging system, effectively doubling the depth of field and unifying the lateral resolution compared to the Gaussian beam quasi-optical system. Moreover, a THz image restoration algorithm based on local gradients and convolution kernel priors is proposed to eliminate further the convolution effect introduced by the Bessel beam, thereby enhancing the lateral resolution to 2 mm. It effectively improves the image under-restoration or over-restoration caused by the mismatch between the ideal and actual point spread function. The imaging results of the resolution test target and semiconductor device verify the advantages of the proposed system and algorithm.
Compact wavemeter incorporating femtosecond laser-induced surface nanostructures enabled by deep learning
Authors: Cai Rui , Xiao Yao , Sui Xiaolin , Li Yongyi , Wu Ziyan , Wu Jie , Deng Guoliang , Zhou Hao , Zhou Shouhuan 
Published: June 2023

Miniature spectrometers have the advantage of high portability and
integration, making them quick and easy to use in various working
environments. The speckle patterns produced by light scattering
through a disordered medium are highly sensitive to wavelength changes
and can be used to design high-precision wavemeters and spectrometers.
In this study, we used a self-organized, femtosecond laser-prepared
nanostructure with a characteristic size of approximately 30–50 nm on
a sapphire surface as a scattering medium to effectively induce
spectral dispersion. By leveraging this random scattering structure,
we successfully designed a compact scattering wavelength meter with
efficient scattering properties. The collected speckle patterns were
identified and classified using a neural network, and the variation of
speckle patterns with wavelength was accurately extracted, achieving a
measurement accuracy of 10 pm in multiple wavelength ranges.
The system can effectively suppress instrument and environmental noise
with high robustness. This work paves the way for the development of
compact high-precision wavemeters.
Updated estimation of cutaneous leishmaniasis incubation period in French Guiana
Authors: Blaizot Romain , Fontaine Albin , Demar Magalie , Delon François , d’Oleon Albane de Bonet , Mayet Aurélie , de Laval Franck , de Santi Vincent Pommier , Briolant Sébastien 
Published: June 2023

Background
The cutaneous leishmaniasis (CL) incubation period (IP) is defined as the time between parasite inoculation by sandfly bite and the onset of the first CL lesion. IP distribution is difficult to assess for CL because the date of exposure to an infectious bite cannot be accurately determined in endemic areas. IP current estimates for CL range from 14 days to several months with a median around 30–60 days, as established by a few previous studies in both New and Old Worlds.

Methodology
We estimated CL incubation period distribution using time-to-event models adapted to interval-censored data based on declared date of travels from symptomatic military personnel living in non-endemic areas that were exposed during their short stays in French Guiana (FG) between January 2001 and December 2021.

Principal findings
A total of 180 patients were included, of which 176 were men (97.8%), with a median age of 26 years. When recorded, the parasite species was always Leishmania guyanensis (31/180, 17.2%). The main periods of CL diagnosis spread from November to January (84/180, 46.7%) and over March-April (54/180, 30.0%). The median IP was estimated at 26.2 days (95% Credible Level, 23.8–28.7 days) using a Bayesian accelerated failure-time regression model. Estimated IP did not exceed 62.1 days (95% CI, 56–69.8 days) in 95% of cases (95th percentile). Age, gender, lesion number, lesion evolution and infection date did not significantly modify the IP. However, disseminated CL was significantly associated with a 2.8-fold shortening of IP.

Conclusions
This work suggests that the CL IP distribution in French Guiana is shorter and more restricted than anticipated. As the incidence of CL in FG usually peaks in January and March, these findings suggest that patients are contaminated at the start of the rainy season.
Severe infections in peritoneal dialysis and home hemodialysis patients: An inception cohort study
Authors: Bitar Wisam , Helve Jaakko , Kanerva Mari , Honkanen Eero , Rauta Virpi , Haapio Mikko , Finne Patrik 
Published: June 2023

ObjectivesInfections are the most common non-cardiovascular cause of death among dialysis patients. Earlier studies have shown similar or higher risk of infectious complications in peritoneal dialysis (PD) compared to hemodialysis (HD) patients, but comparisons to home HD patients have been rare. We investigated the risk of severe infections after start of continuous ambulatory PD (CAPD) and automated PD (APD) as compared to home HD.MethodsAll adult patients (n = 536), who were on home dialysis at day 90 from starting kidney replacement therapy (KRT) between 2004 and 2017 in Helsinki healthcare district, were included. We defined severe infection as an infection with C-reactive protein of 100 mg/l or higher. Cumulative incidence of first severe infection was assessed considering death as a competing risk. Hazard ratios were estimated using Cox regression with propensity score adjustment.ResultsThe risk of getting a severe infection during the first year of dialysis was 35% for CAPD, 25% for APD and 11% for home HD patients. During five years of follow-up, the hazard ratio of severe infection was 2.8 [95% CI 1.6–4.8] for CAPD and 2.2 [95% CI 1.4–3.5] for APD in comparison to home HD. Incidence rate of severe infections per 1000 patient-years was 537 for CAPD, 371 for APD, and 197 for home HD patients. When excluding peritonitis, the incidence rate was not higher among PD than home HD patients.ConclusionsCAPD and APD patients had higher risk of severe infections than home HD patients. This was explained by PD-associated peritonitis.
Reliability and validity of the Forgotten Joint Score-12 for total ankle replacement and ankle arthrodesis
Authors: Noguchi Koji , Yamaguchi Satoshi , Teramoto Atsushi , Amaha Kentaro , Kanzaki Noriyuki , Tanaka Hirofumi , Yasui Tetsuro , Inaba Yosuke 
Published: June 2023

Objectives
This study evaluated the reliability and validity of the Forgotten Joint Score-12 (FJS-12)—a measure of patients’ ability to forget their joints in daily life—in patients who underwent total ankle replacement (TAR) or ankle arthrodesis (AA).

Methods
Patients who underwent TAR or AA were recruited from seven hospitals. The patients completed the Japanese version of FJS-12 twice, at an interval of two weeks, at a minimum of one year postoperatively. Additionally, they answered the Self-Administered Foot Evaluation Questionnaire and EuroQoL 5-Dimension 5-Level as comparators. The construct validity, internal consistency, test-retest reliability, measurement error, and floor and ceiling effects were evaluated.

Results
A total of 115 patients (median age, 72 years), comprising 50 and 65 patients in the TAR and AA groups respectively, were evaluated. The mean FJS-12 scores were 65 and 58 for the TAR and AA groups, respectively, with no significant difference between groups (P = 0.20). Correlations between the FJS-12 and Self-Administered Foot Evaluation Questionnaire subscale scores were good to moderate. The correlation coefficient ranged from 0.39 to 0.71 and 0.55 to 0.79 in the TAR and AA groups, respectively. The correlation between the FJS-12 and EuroQoL 5-Dimension 5-Level scores was poor in both groups. The internal consistency was adequate, with Cronbach’s α greater than 0.9 in both groups. The intraclass correlation coefficients of test-retest reliability was 0.77 and 0.98 in the TAR and AA groups, respectively. The 95% minimal detectable change values were 18.0 and 7.2 points in the TAR and AA groups, respectively. No floor or ceiling effect was observed in either group.

Conclusions
The Japanese version of FJS-12 is a valid and reliable questionnaire for measuring joint awareness in patients with TAR or AA. The FJS-12 can be a useful tool for the postoperative assessment of patients with end-stage ankle arthritis.
Speech-in-noise performance in objectively determined cochlear implant maps, including the effect of cognitive state
Authors: Yiannos Jessica M. , Bester Christofer W. , Zhao Christopher , Gell Barbara , Jayakody Dona M. P. 
Published: June 2023

Objective
Cochlear Implant (CI) programming based on subjective psychophysical fine-tuning of loudness scaling involves active participation and cognitive skills and thus may not be appropriate for difficult-to-condition populations. The electrically evoked stapedial reflex threshold (eSRT) is an objective measure that is suggested to provide clinical benefit to CI programming. This study aimed to compare speech reception outcomes between subjective and eSRT objectively determined CI maps for adult MED-EL recipients. The effect of cognitive skills on these skills was further assessed.

Methods
Twenty-seven post lingually hearing-impaired MED-EL CI recipients were recruited, 6 with mild cognitive impairment (MCI– 4 male, 79 years ± 5), 21 with normal cognitive function (5 male, 63 years ± 12). Two MAPs were generated: a subjective MAP and an objective MAP in which eSRTs determined maximum comfortable levels (M-Levels). Participants were randomly divided into two groups. Group A trialled the objective MAP for two weeks before returning for outcome assessment. During the following two weeks, Group A trialled the subjective MAP before returning for outcome assessment. Group B trialled MAPs in reverse. Outcome measures included the Hearing Implant Sound Quality Index (HISQUI), Consonant-Nucleus-Consonant (CNC) word test, and Bamford-Kowal-Bench Speech-in-Noise (BKB-SIN) test.

Results
eSRT based MAPS were obtained in 23 of the participants. A strong relationship was demonstrated between global charge between eSRT-based and psychophysical-based M-Levels (r = 0.89, p < .001). The Montreal Cognitive Assessment for the Hearing Impaired (MoCA-HI) testing identified 6 CI recipients with MCI (MoCA-HI total score ≤23). The MCI group was older (63, 79 years), but were not otherwise different in sex, duration of hearing loss or duration of CI use. For all patients, no significant differences were found for sound quality or speech in quiet scores between eSRT-based and psychophysical-based MAPs. However, psychophysically determined MAPs showed significantly better speech-in-noise reception (6.74 vs 8.20-dB SNR, p = .34). MoCA-HI scores showed a significant, moderate negative correlation with BKB SIN for both MAP approaches (Kendall’s Tau B, p = .015 and p = .008), with no effect on the difference between MAP approaches.

Conclusion
Results indicate eSRT-based methods provide poorer outcomes than psychophysical-based method. While speech-in-noise reception is correlated with MoCA-HI score, this affected both behaviourally and objectively determined MAPs. The results suggest fair confidence in the eSRT-based method as a guide for setting M-Level for difficult-to-condition CI populations in simple listening conditions.
Prediction of local recurrence in tenosynovial giant cell tumor of the knee: Based on preoperative MRI evaluation into disease subtypes and severity
Authors: Kim Jun-Ho , Lee Seul Ki , Kim Jee-Young 
Published: June 2023

Objective
Tenosynovial giant cell tumors (TSGCTs) of the knee differ in their clinical outcome according to disease subtypes and severity. The aim of this study was to determine the predictive MRI features related to local recurrence in TSGCT of the knee regarding disease subtypes and severity.

Methods
This retrospective study included 20 patients with pathology-proven TSGCT of the knee who underwent preoperative MRI and surgery from Jan. 2007 to Jan. 2022. The anatomical point of the lesion was determined with a knee mapping. And then MRI features related to disease subtype including nodularity (single vs. multinodular); margin (circumscribed vs. infiltrative); peripheral hypointenseity (present vs. absent); internal hypointensity reflecting hemosiderin deposition (speckled vs. granular) were assessed. Third, MRI features related to disease severity including involvement of bone, cartilage, and tendon were evaluated. MRI features for predicting local recurrence of TSGCT were tested using chi-square test and logistic regression analysis.

Results
Ten patients with diffuse-type TSGCT (D-TSGCT) and 10 patients with localized-type TSGCT (L-TSGCT) were included. There were six cases of local recurrence and all of them were D-TSGCT and none for L-TSGCT with statistical difference (P = 0.015). D-TSGCT that was direct risk factor for local recurrence showed more multinodular (80.0% vs. 10.0%; P = 0.007), infiltrative margin (90.0% vs. 10.0%; P = 0.002), and absent peripheral hypointensity (100.0% vs. 20.0%; P = 0.001) than L-TSGCT. Multivariate analysis showed infiltrative margin (odds ratio [OR], 81.0; P = 0.003) was independent MRI factor for D-TSGCT. Disease severity for risk of local recurrence included cartilage (66.7% vs. 7.1%; P = 0.024) and tendon (100.0% vs. 28.6%; P = 0.015) involvement compared to no local recurrence. Multivariate analysis showed tendon involvement (OR, 12.5; P = 0.042) was predictive MRI parameter for local recurrence. By combining tumor margin and tendon involvement, local recurrence was predicted sensitively on preoperative MRI (sensitivity, 100%; specificity, 50%; accuracy, 65%).

Conclusion
D-TSGCTs was associated with local recurrence and showed multinodularity infiltrative margin, and absent peripheral hypointensity. Disease severity including cartilage and tendon involvement was associated with local recurrence. Preoperative MRI evaluation by combining disease subtypes and severity can predict local recurrence sensitively.