bluuebunny/crossref_metadata_2025 huggingface dataset:
Gender differences in the association between anemia and osteoporosis: findings from a large-scale prospective analysis
Authors: Huang Yanjun , Huang Cheng , Shen Yanzhu , Zhang Qidong , Dai Jinzhu , Xiong Wenjing , Tang Xiangsheng , Yi Ping , Lin Jun
Published: July 2024

Purpose

Osteoporosis (OP) is characterized by a gradual onset and an increased susceptibility to osteoporotic fractures. Previous retrospective studies have suggested that hemoglobin (HGB) levels could be a potential diagnostic marker for OP. However, the relationship between OP and anemia remains uncertain. This prospective study aimed to investigate the association between HGB levels and OP.

Methods

Leveraging data from the UK Biobank, a cohort of 452 778 individuals was analyzed. Employing a modified Cox proportional hazards model that accounted for sociodemographic factors, lifestyle, and health-related factors, we examined the links between incident OP and sex. Moreover, we investigated the impact of OP with or without a pathological fracture.

Results

Following a median follow-up period of 5.85 years, 4294 participants were diagnosed with OP. After adjusting for a comprehensive range of pertinent confounders, individuals with anemia exhibited a 2.15-fold higher risk of OP in males and a 1.41-fold higher risk in females. Moreover, each unit increase in HGB concentration corresponded to a 0.83-fold decrease in OP risk for men and a 0.94-fold decrease for women.

Perspectives

Our findings reveal a significant correlation between HGB levels or anemia and OP, with males demonstrating a greater susceptibility compared to females. The risk of OP decreased with higher HGB concentrations in both sexes, although this effect was more pronounced in males. It is recommended to conduct longitudinal studies to investigate the causality of the observed connections and experimental studies to understand the underlying mechanisms.
Sex-specific associations between habitual snoring and cancer prevalence: insights from a US Cohort Study
Authors: Ding Qinglan , Herrin Jeph , Kryger Meir
Published: July 2024

Study Objectives

To investigate the sex-specific association between habitual snoring and overall cancer prevalence and subtypes, and to examine the influence of age, body mass index (BMI), and sleep duration on this association.

Methods

This study utilized data from the National Health and Nutrition Examination Survey cycles between 2005 and 2020 and included 15 892 participants aged 18 and over. We employed inverse probability of treatment weighting based on propensity scores to adjust for confounders when comparing the prevalence of cancer between habitual snorers and non-habitual snorers for each sex and cancer type. Subgroup analyses were conducted based on sleep duration, age, and BMI categories.

Results

The cohort (mean age 48.2 years, 50.4% female, and 30.5% habitual snorers) reported 1385 cancer cases. In men, habitual snoring was linked to 26% lower odds of any cancer (OR 0.74, 95% CI: 0.66 to 0.83), while in women, it showed no significant difference except lower odds of breast cancer (OR 0.77, 95% CI: 0.63 to 0.94) and higher odds of cervix cancer (OR 1.54, 95% CI: 1.18 to 2.01). Age and sleep duration significantly influenced the snoring-cancer relationship, with notable variations by cancer type and sex.

Conclusions

Habitual snoring exhibits sex-specific associations with cancer prevalence, showing lower prevalence in men and varied results in women. These findings emphasize the critical need for further research to uncover the biological mechanisms involved. Future investigations should consider integrating sleep characteristics with cancer prevention and screening strategies, focusing on longitudinal research and the integration of genetic and biomarker analyses to fully understand these complex relationships.
Inferring Taxonomic Affinities and Genetic Distances Using Morphological Features Extracted from Specimen Images: A Case Study with a Bivalve Data Set
Authors: Hofmann Martin , Kiel Steffen , Kösters Lara M , Wäldchen Jana , Mäder Patrick
Published: July 2024

Reconstructing the tree of life and understanding the relationships of taxa are core questions in evolutionary and systematic biology. The main advances in this field in the last decades were derived from molecular phylogenetics; however, for most species, molecular data are not available. Here, we explore the applicability of 2 deep learning methods—supervised classification approaches and unsupervised similarity learning—to infer organism relationships from specimen images. As a basis, we assembled an image data set covering 4144 bivalve species belonging to 74 families across all orders and subclasses of the extant Bivalvia, with molecular phylogenetic data being available for all families and a complete taxonomic hierarchy for all species. The suitability of this data set for deep learning experiments was evidenced by an ablation study resulting in almost 80% accuracy for identifications on the species level. Three sets of experiments were performed using our data set. First, we included taxonomic hierarchy and genetic distances in a supervised learning approach to obtain predictions on several taxonomic levels simultaneously. Here, we stimulated the model to consider features shared between closely related taxa to be more critical for their classification than features shared with distantly related taxa, imprinting phylogenetic and taxonomic affinities into the architecture and training procedure. Second, we used transfer learning and similarity learning approaches for zero-shot experiments to identify the higher-level taxonomic affinities of test species that the models had not been trained on. The models assigned the unknown species to their respective genera with approximately 48% and 67% accuracy. Lastly, we used unsupervised similarity learning to infer the relatedness of the images without prior knowledge of their taxonomic or phylogenetic affinities. The results clearly showed similarities between visual appearance and genetic relationships at the higher taxonomic levels. The correlation was 0.6 for the most species-rich subclass (Imparidentia), ranging from 0.5 to 0.7 for the orders with the most images. Overall, the correlation between visual similarity and genetic distances at the family level was 0.78. However, fine-grained reconstructions based on these observed correlations, such as sister–taxa relationships, require further work. Overall, our results broaden the applicability of automated taxon identification systems and provide a new avenue for estimating phylogenetic relationships from specimen images.
Effect of beef heifer development systems utilizing corn residue and late summer planted cover crops on growth, reproductive performance, and economics
Authors: Speer Hannah F , Cushman Robert A , Freetly Harvey C , Parsons Jay , Windh Jessica , Drewnoski Mary E
Published: July 2024

The objective of this study was to evaluate growth and reproductive performance of heifers developed using 3 different winter systems in the midwestern U.S. Spring-born heifers (n = 1,156; 214 d of age; SD ± 17 d) were used in a 3-yr study to evaluate performance in winter development systems, which utilized cover crop (CC) and corn residue grazing. Heifers were assigned to 1 of 3 treatments: grazing corn residue with 0.77 kg/d dried distillers grains (CD) or 1.69 kg/d wheat midds (CW) supplementation followed by a grower ration in the drylot, or grazing late summer planted oat-brassica CC followed by corn residue grazing with 0.35 kg/d dried distillers grains supplementation (CC). Supplementation during the corn residue phase was targeted to result in a common body weight (BW) (276 kg; ~45% of mature BW) by the end of the winter development period. Grazing of corn residue (CD and CW) and CC began in early November. After 63 d, heifers assigned to CC were moved to corn residue; on day 77 heifers assigned to CD and CW began receiving a grower ration in the drylot. In mid-February (day 98), heifers were comingled and managed in a single group. Breeding season began in June and lasted for 29 d. The ADG of heifers assigned to CC when grazing CC (days 1 to 63) was greater (0.76 kg/d; P < 0.01) than those assigned to CD or CW (0.58 kg/d and 0.49 kg/d, respectively). Gain during the last 35 d of the winter period for heifers assigned to CC (0.36 kg/d) was less (P < 0.01) than those assigned to CW (0.49 kg/d) but not different from CD heifers (0.41 kg/d). Overall (days 1 to 98), winter ADG was greater (P < 0.05) for heifers assigned to CC (0.62 kg/d) than CD (0.53 kg/d) or CW (0.50 kg/d), which did not differ (P = 0.42). Percent of mature BW in May (27 d pre-breeding) was greater (P < 0.01) for heifers assigned to CC (52%) than for those on CD and CW (50%), which did not differ (P = 0.64). Pregnancy rates were affected by treatment (P < 0.03), with heifers assigned to CC (76%) being greater than CW (64%) and CD heifers being intermediate (70%). When accounting for the differences in cost and the value of open and bred heifers, the economic return tended to differ (P = 0.07) among treatments, with CC and CW not differing (P ≥ 0.20) from CD but return for CC being $73 greater than CW (P = 0.02). Utilizing oat-brassica CCs early in the winter followed by a slower rate of gain while grazing corn residue with distillers supplementation appears to be as effective for developing beef heifers in the midwestern U.S. as supplementing distillers grains.
Xylem sap residue in cut-open conduits can affect gas discharge in pneumatic experiments
Authors: Miranda Marcela T , Pereira Luciano , Pires Gabriel S , Guan Xinyi , Silva Luciano M , Kreinert Swetlana , Machado Eduardo C , Jansen Steven , Ribeiro Rafael V
Published: July 2024

Considerable attention has been paid to addressing methodological concerns related to measurements of embolism in conduits of angiosperm xylem. A fast, easy and cheap method is based on gas extraction measurements from dehydrating samples to obtain pneumatic vulnerability curves (VCs). Here, we tested the assumption that cutting open conduits leads to gas-filled lumina when these are cut in air at fairly high water potentials, which is required to detect embolism in intact conduits. We performed VCs with the Pneumatron for 12 angiosperm species and extracted sap from cut-open vessels in branches of nine species under early stages of branch dehydration. The optical method was applied to Citrus plants as an alternative reference method to estimate embolism resistance. We found an increase in gas discharge during early stages of dehydration, which affected the pneumatic VCs for most of the species studied. Xylem sap residue was not absorbed immediately by surrounding tissue in cut-open conduits in six of the nine species but gradually disappeared over time during progressive dehydration. The amount of gas discharged increased until all residual sap was absorbed, and was not related to embolism. We conclude that residual xylem sap in cut-open conduits affects early stages of pneumatic VCs and represents a novel artifact that can easily be corrected for. Yet, it remains unclear why exactly the air–water meniscus in cut-open conduits did not fully withdraw to the conduit end wall in most species. By analyzing the slope of VCs over time, we could improve estimations of embolism resistance, as evidenced by a strong agreement between the pneumatic and the optical methods. Since residual sap in cut-open conduits of some species could slightly underestimate embolism resistance, we propose to apply a correction for this artifact based on the high time-resolution measurements taken with a Pneumatron.
Intraspecific variation in photosynthetic thermal acclimation in Fagus crenata seedlings from two populations growing at different elevations in northern Japan
Authors: Akaji Yasuaki , Torimaru Takeshi , Akada Shinji
Published: July 2024

Plants can acclimate their photosynthesis to growth temperature, but the contribution of local adaptation to intraspecific variation in thermal acclimation of photosynthesis is not fully understood. Here, we experimentally investigated the photosynthetic thermal acclimation in Fagus crenata Blume seedlings from two populations growing at different elevations and temperature regimes (low- and high-elevation sites) in northern Japan. We acclimated seedlings for 14 to 23 days at daytime temperatures of either 22 °C (control) or 27 °C (warm treatment) and obtained photosynthetic temperature–response curves in the range of 19 to 32 °C. The optimum temperature of photosynthesis (Topt) was ~0.6 °C higher in seedlings acclimated at 27 °C than in those acclimated at 22 °C, and it was significantly lower in seedlings with higher stomatal sensitivity to leaf-to-air vapor pressure deficit than in those with lower sensitivity. The effects of warm treatment, population and treatment–population interaction on Topt were not significant in the two-way analysis of variance, but the effect of treatment became significant when stomatal sensitivity to leaf-to-air vapor pressure deficit was included as a covariate in the model. Structural equation modeling indicated that seedlings with lower root biomass had lower Topt because of the high stomatal sensitivity to leaf-to-air vapor pressure deficit. Structural equation modelling also indicated that the way of shifting the Topt differed between the two populations: seedlings from a high-elevation site depended on decreasing photosynthetic rates at low temperatures for the increase in Topt but seedlings from a low-elevation site did not. We suggest that the difference in thermal acclimation of photosynthesis between the two populations may reflect adaptation to different climate regimes and that belowground traits should be considered when investigating thermal acclimation capacity, especially in seedlings.
Sustainable development clauses in international contracts through the lens of the Unidroit principles
Authors: Pannebakker Ekaterina
Published: July 2024

Most transactions that leave an imprint on the environment and communities are organized by commercial contracts. However, little is known about the way in which parties reflect sustainable development in contractual clauses. How can parties to international contracts commit to respect sustainable development goals? What are the possible degrees of commitment? Which contractual mechanisms can apply to the monitoring of compliance? How does one establish a link between the failure to meet sustainable development goals and the contractual liability or termination of contract? This article identifies contractual clauses relating to sustainable development and analyses these clauses through the lens of the 2016 International Institute for the Unification of Private Law (Unidroit) Principles of International Commercial Contracts (PICC). Drawing inspiration from open access contracts, the analysis will demonstrate that Article 1.8 of the PICC, precluding inconsistent behaviour, and Articles 5.1.4 and 5.1.5, on the duty of best efforts and the obligation to achieve a specific result, as well as the provisions on liability, can assist contract drafters, judges, and arbitrators in drafting and interpreting such clauses.
Support for Mail-Order Pharmacy Dispensing of Mifepristone for Medication Abortion
Authors: Rosenberg Karen
Published: July 2024

According to this study:
More than a new name
Authors: Wrynn Alexander F.
Published: July 2024

Infections from Clostridioides difficile (often called C. diff) have long presented challenges for both patients and clinicians. Traditionally, C. diff has been considered a nosocomial infection, but in recent years, a noticeable spike in community-acquired cases has occurred. C. diff infection (CDI) testing is often complicated, as various testing options with differing sensitivity and specificity for active infection are available. Also, recent guideline changes have altered the recommended treatment of infection. This article discusses recent changes to both the diagnosis and management of CDI and how they can be applied to everyday NP practice.
Screw Motion Used in Semiconstrained Rotational Plate Systems for Anterior Cervical Discectomy and Fusion
Authors: Tatara Yasunori , Niimura Takanori , Sakaguchi Akira , Katayama Hiroki , Miyaoka Yoshinari , Mihara Hisanori
Published: July 2024

Study Design:

Retrospective observational study.

Objective:

To scrutinize screw motion used in semiconstrained rotational plate systems for anterior cervical discectomy and fusion (ACDF).

Summary of Background Data:

Semiconstrained rotational plate systems are supposed to control graft subsidence and facilitate lordosis acquisition and maintenance by toggling the instrumented vertebrae via variable-angle screws. However, their benefits may be unrealized if the screws move within the vertebrae.

Methods:

We reviewed medical records of 119 patients who underwent 1-level, 2-level, 3-level, or 4-level ACDF, divided them into the short-segment (n=62, 1-level or 2-level ACDF) and long-segment (n=59, 3- level or 4-level ACDF) groups, and investigated their immediate and 1-year postoperative lateral radiographs. We measured the fused segmental angle, screw angles at the upper-instrumented vertebra (UIV) and lower-instrumented vertebra (LIV), distance from the screw base to the endplate of UIV/LIV (SBE), and distance from the screw tip to the endplate of UIV/LIV (STE) to analyze the screw motion used in these plate systems. The differences between the immediate and 1-year postoperative values were statistically analyzed. The nonunion level was also investigated.

Results:

Screw angle and SBE at the LIV significantly decreased in the long-segment group (−14.5±9.8 degrees and −2.8±1.8 mm, respectively) compared with those in the short-segment group (−4.6±6.0 degrees and −1.0±1.5 mm, respectively). Thus, the long-segment group could not maintain the immediate-postoperative segmental angle. Overall, 27 patients developed nonunion, with 19 (70.4%) in the long-segment group and 21 (77.8%) at the lowest fused level.

Conclusions:

Semiconstrained rotational plate systems provide only vertical forces to the fused segment rather than toggling the instrumented vertebrae. Postoperatively in multilevel ACDF, LIV screws migrate caudally, suggesting that these plate systems are not always effective in maintaining lordosis. Moreover, LIV screws and the anterior wall of the LIV are subject to overloading, resulting in a high rate of nonunion at the lowest fused level.

Level of Evidence:

Level III.
Methods to Track Effective Doses from Airborne Radioactive Emissions for Compliance with 40 CFR 61, SUBPART H
Authors: Harshman Amber M. , McCarter William L.
Published: July 2024

US Department of Energy national laboratories can play an integral role in not only the advancement of science but also in the treatment of various medical conditions through research and development activities conducted at radioisotope production facilities. A project has been underway at Oak Ridge National Laboratory since 2016 whose mission is to produce and supply the radioisotope 227Ac, which is used in a radiopharmaceutical developed to treat certain types of prostate cancer and bone metastases. Production activities result in the environmental release of airborne radioactive emissions, which are governed by Clean Air Act regulations described in 40 CFR Part 61, Subpart H. Stack 3039, the source that emits radioactive effluents from 227Ac production, is subject to additional requirements outlined in American National Standards Institute (ANSI) N13.1-1969 due to its grandfathered status. Radioactive emissions are limited to levels below those that would cause annual compliance dose standards for members of the public to be exceeded and stack 3039 to lose its grandfathered status. To allow for maximum production of 227Ac without exceeding relevant dose limits, monthly tracking of project emissions and resulting CAP88-PC modeled effective doses to a maximally exposed individual have been implemented. Four years of tracking data were compiled and analyzed to identify additional methods that could be used to estimate project doses more frequently, potentially further optimizing 227Ac production while maintaining compliance with applicable regulations.
Postprocedural infection rate after minor surgical procedures performed with and without sterile gloves: a systematic review and meta-analysis
Authors: Shrestha Oshan , Basukala Sunil , Bhugai Nabaraj , Bohara Sujan , Bhatt Ayush , Thapa Niranjan , Paudel Sushanta , Joshi Niraj , Mehta Bipin , Acharya Astutee , Shrestha Nirakar
Published: July 2024

Introduction:

Postprocedural infection has been a top priority for the perioperative team. The use of sterile gloves to counter this became popular and was routinely used, but randomized studies have shown that the benefit that was thought to be added by the use of sterile gloves is insignificant and that not all procedures require the use of sterile gloves.

Methods:

Prospective protocol registration was and electronic databases were searched without using any search filters. Screening was performed by independent reviewers, and data was extracted from selected studies. Heterogeneity was assessed by the I
2 test, and the effect model was chosen accordingly. The odds ratio was used as an effect measure as the variables in this study were dichotomous. Forest plots and funnel plots were used to give visual feedback.

Results:

This meta-analysis included 14 comparative studies that involved a total of 12,625 patients. Analysis of postprocedural infection outcome showed no significant difference between the procedure performed using sterile gloves and without using sterile gloves (OR: 0.88; 95% CI: 0.71–1.10; n=12,625; I
2=0%; P-value=0.26). Sensitivity analysis and subgroup analysis for randomized studies only, surgical site infection, and patients that did not receive prophylactic antibiotics showed no variations. The use of sterile gloves did not show any extra benefit for controlling infection during wound repair, excision and suturing, cystoscopy, and urinary catheterization.

Conclusion:

The use of sterile gloves does not have any extra benefit for preventing infections when minor surgical procedures are performed.
A Case study of polypharmacy-induced serotonin syndrome in a cancer patient
Authors: Zhu Andrew , Kuhnly Nicole , Chen Leon , Dulu Alina O.
Published: July 2024

Polypharmacy in cancer care can be complex and detrimental, particularly among younger patients, who can be easily overlooked. This report showcases a 54-year-old woman with cancer, treated for dapsone-induced methemoglobinemia with methylene blue (MB), subsequently developing serotonin syndrome (SS) due to concurrent serotonin-active medications. This case highlights the critical impact of polypharmacy, emphasizing the necessity for acute care providers to diligently assess medication interactions, especially in emergencies. It underscores the importance of considering alternative treatments and the vigilant monitoring of symptoms indicative of adverse drug interactions to ensure patient safety and optimize outcomes in complex therapeutic scenarios.
A Quantitative Study of the Head Pitching Test for Lateral Canal BPPV
Authors: Califano Luigi , Martellucci Salvatore , Melillo Maria Grazia
Published: July 2024

Objectives

Lateral semicircular canal BPPV (LSC-BPPV) is diagnosed with the Head Yaw Test (HYT) by observing nystagmus direction and comparing the nystagmus intensity on both sides according to Ewald’s laws. Head Pitching Test (HPT) is a diagnostic maneuver performed in the upright position by bending the patient’s head forward (bowing) and backward (leaning) and observing the evoked nystagmus. We aimed to assess the sensitivity of HPT in correctly diagnosing LSC-BPPV through the quantitative measurement of Bowing and Leaning nystagmus slow-phase velocity (SPV).

Methods

One hundred cases of LSC-BPPV were prospectively enrolled. HPT was performed, looking for pseudospontaneous, bowing, and leaning nystagmus. HYT was considered for the “final diagnosis.” HPT was defined as “diagnostic” if the nystagmus was present in at least one position, “undiagnostic” if no nystagmus was detectable. The direction and the SPV of nystagmus in all positions were analyzed and compared to determine the degree of agreement between HPT and HYT.

Outcomes

Sixty-four geotropic and 36 apogeotropic forms were diagnosed. HPT was diagnostic in 80 cases, with no difference between the two forms. According to Ewald’s laws, the direction of stronger nystagmus evoked by HPT agreed with the HYT results in 39/52 (75%) cases in geotropic forms and 21/28 (75%) cases in apogeotropic forms. The agreement between HPT and HYT was “substantial” considering all the cases and “almost complete” considering only the patients with diagnostic HPT.

Conclusion

Quantitative HPT is a valid test in diagnosing the affected side and form of LSC-BPPV, even if less reliable than HYT.
Amplitude Parameters Are Predictive of Hearing Preservation in a Randomized Controlled Trial of Intracochlear Electrocochleography During Cochlear Implant Surgery
Authors: Harris Michael S. , Koka Kanth , Thompson-Harvey Adam , Harvey Erin , Riggs William J. , Saleh Shaza , Holder Jordan T. , Dwyer Robert T. , Prentiss Sandra M. , Lefler Shannon M. , Kozlowski Kristin , Hiss Meghan M. , Ortmann Amanda J. , Nelson-Bakkum Erin R. , Büchner Andreas , Salcher Rolf , Harvey Steven A. , Hoffer Michael E. , Bohorquez Jorge E. , Alzhrani Farid , Alshihri Rana , Almuhawas Fida , Danner Christopher J. , Friedland David R. , Seidman Michael D. , Lenarz Thomas , Telischi Fred F. , Labadie Robert F. , Buchman Craig A. , Adunka Oliver F.
Published: July 2024

Objective

To prospectively evaluate the association between hearing preservation after cochlear implantation (CI) and intracochlear electrocochleography (ECochG) amplitude parameters.

Study Design

Multi-institutional, prospective randomized clinical trial.

Setting

Ten high-volume, tertiary care CI centers.

Patients

Adults (n = 87) with sensorineural hearing loss meeting CI criteria (2018–2021) with audiometric thresholds of ≤80 dB HL at 500 Hz.

Methods

Participants were randomized to CI surgery with or without audible ECochG monitoring. Electrode arrays were inserted to the full-depth marker. Hearing preservation was determined by comparing pre-CI, unaided low-frequency (125-, 250-, and 500-Hz) pure-tone average (LF-PTA) to LF-PTA at CI activation. Three ECochG amplitude parameters were analyzed: 1) insertion track patterns, 2) magnitude of ECochG amplitude change, and 3) total number of ECochG amplitude drops.

Results

The Type CC insertion track pattern, representing corrected drops in ECochG amplitude, was seen in 76% of cases with ECochG “on,” compared with 24% of cases with ECochG “off” (p= 0.003). The magnitude of ECochG signal drop was significantly correlated with the amount of LF-PTA change pre-CI and post-CI (p< 0.05). The mean number of amplitude drops during electrode insertion was significantly correlated with change in LF-PTA at activation and 3 months post-CI (p≤ 0.01).

Conclusions

ECochG amplitude parameters during CI surgery have important prognostic utility. Higher incidence of Type CC in ECochG “on” suggests that monitoring may be useful for surgeons in order to recover the ECochG signal and preventing potentially traumatic electrode–cochlear interactions.
A Population-based Study Investigating the Incidence of Human Papillomavirus–Associated and Human Papillomavirus–Independent Cervical Adenocarcinomas
Authors: Ben-Mussa Ali , Shah Rajeev , Rajendran Simon , McCluggage W. Glenn
Published: July 2024

Cervical adenocarcinomas are now classified as human papillomavirus (HPV)-associated and HPV-independent types with the former being more common. However, population-based studies regarding the relative incidences of the 2 types are few. This study investigates the incidence of cervical adenocarcinomas in Northern Ireland (a country with a relatively stable population of ~1.8 million) over a recent 9-year period (2015–2023). Overall, there were 146 primary cervical adenocarcinomas, 130 HPV-associated (89%) and 16 HPV-independent (11%). The median age was 43 years (range: 24–82) for HPV-associated and 62.5 years (range: 31–84) for HPV-independent neoplasms; this was statistically significant (P < 0.001). The calculated age-adjusted incidence of the patients with HPV-associated and HPV-independent neoplasms was 1.68 and 0.20 per 100,000 person-years, respectively. The HPV-independent neoplasms were more often advanced stage at diagnosis; 97 of 130 (75.4%) of the HPV-associated cases were diagnosed at Stage I compared with 5 of 16 (31.3%) of the HPV-independent cases. The HPV-independent neoplasms were mostly gastric-type (56.3%) with smaller numbers of clear cells and mesonephric. Despite the relatively short follow-up, the mortality of patients with HPV-independent adenocarcinomas was significantly higher than patients with HPV-associated neoplasms (56.3% vs 5.4%) with a median survival of just over a year (13.2 mo) in the former for those who died.
Translation and Comprehensive Validation of the Hebrew Survey on Patient Safety Culture (HSOPS 2.0)
Authors: Ein-Gal Yaffa , Sela Roni , Arad Dana , Szyper Kravitz Martine , Hanhart Shuli , Goldschmidt Nethanel , Kedmi-Shahar Efrat , Bitan Yuval
Published: July 2024

Objectives

The study aim was to create an updated valid translation into Hebrew of the AHRQ’s survey on patient safety culture for hospitals, version 2.0. It also suggested a supplementary section about workers’ safety. Comparable and valid measurement tools are important for national and international benchmarking of patient safety culture in hospitals.

Methods

The process was carried out by a designated committee according to AHRQ translation guidelines. Methodology included several translation cycles, 6 semistructured cognitive interviews with health workers, and a web-based pilot survey at 6 general hospitals. Main analyses included an exploratory factor analysis, a comparison of the differences in results between versions 1 and 2 of the survey to the differences reported by AHRQ, and content analysis of open-ended questions.

Results

A total of 483 returned questionnaires met the inclusion criterion of at least 70% completion of the questionnaire. The demographic distributions suggested this sample to be satisfactory representative. Cronbach’s alpha for the translated questionnaire was 0.95, meaning a high internal consistency between the survey items. An exploratory factor analysis revealed 8 underlying factors, and a secondary analysis further divided the first factor into 2 components. The factors structure generally resembled HSOPS 2.0 composite measures. Analyses of the new section about health workers’ safety showed high involvement and possible common themes.

Conclusions

The study demonstrated good psychometric properties—high reliability and validity of the new translated version of the questionnaire. This paper may serve other countries who wish to translate and adapt the safety culture survey to different languages.
Collaboration of Surgeons and Speech Pathologists in the Selection of Optimal Treatment; Role of Speech Pathologist and Audiologist in the Interdisciplinary Management of Patients With Clefts
Authors: Muller John N. , Volk Angela S. , Hollier Larry H.
Published: July 2024

Children born with cleft lip and/or cleft palate may have problems with feeding, speech, and hearing. Collaboration of surgeons and speech pathologists guide cleft care treatment decisions and vary throughout the cleft timeline. This review aims to discuss the role of the speech pathologist and audiologist in the interdisciplinary management of patients with cleft lip and palate, specifically, how the speech pathologists’ findings guide surgical decision-making.
Aurantiacibacter hainanensis sp. nov. and Qipengyuania zhejiangensis sp. nov., two novel Erythrobacteraceae species isolated from tidal flat sediments
Authors: Liu Wen-Jia , Zhang Yu , Cao Ke , Li Jia-Xi , Wen Yu-Qiao , Sun Cong , Xu Lin
Published: July 2024

Two Gram-stain-negative, rod-shaped, non-motile, aerobic and carotenoid-producing strains, belonging to the family Erythrobacteraceae, designated as H149T and Z2T, were isolated from tidal flat sediment samples collected in Hainan and Zhejiang, PR China, respectively. Growth of strain H149T occurred at 15–42 °C, 0–10.0 % (w/v) NaCl, and pH 6.0–8.5, with the optima at 35–37 °C, 3.0–3.5 % (w/v) NaCl and pH 7.0. Strain Z2T grew at 15–37 °C, 0–6.0 % (w/v) NaCl, and pH 6.0–9.5, with the optima at 25–30 °C, 0.5–1.0 % (w/v) NaCl and pH 6.0–6.5. Ubiquinone-10 was the sole ubiquinone in two strains. The predominant cellular fatty acids of strain H149T were C16 : 0, summed feature 3 and summed feature 8, while those of strain Z2T were C17 : 1
 ω6c, summed feature 3 and summed feature 8. Strains H149T and Z2T shared diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine and sphingoglycolipid as major polar lipids. The 16S rRNA gene sequence identity analysis indicated that strain H149T had the highest sequence identity of 98.4 % with Aurantiacibacter odishensis KCTC 23981T, and strain Z2T had that of 98.2 % with Qipengyuania pacifica NZ-96T. Phylogenetic trees based on 16S rRNA gene and core-genome sequences revealed that strains H149T and Z2T formed two independent clades in the genera Aurantiacibacter and Qipengyuania, respectively. Strain H149T had average nucleotide identity values of 74.0–81.3 % and in silico DNA–DNA hybridization values of 18.5–23.1 % with Aurantiacibacter type strains, while strain Z2T had values of 73.3–78.7 % and 14.5–33.3 % with Qipengyuania type strains. The genomic DNA G+C contents of strains H149T and Z2T were 64.3 and 61.8 %, respectively. Based on the genetic, genomic, phylogenetic, physiological and chemotaxonomic results, strains H149T (=KCTC 8397T=MCCC 1K08920T) and Z2T (=KCTC 8396T=MCCC 1K08946T) are concluded to represent two novel Erythrobacteraceae species for which the names Aurantiacibacter hainanensis sp. nov. and Qipengyuania zhejiangensis sp. nov. are proposed, respectively.
Ensemble Refinement of mismodeled cryo-EM RNA Structures Using All-Atom Simulations
Authors: Posani Elisa , Janos Pavel , Haack Daniel , Toor Navtej , Bonomi Massimiliano , Magistrato Alessandra , Bussi Giovanni
Published: July 2024

The advent of single-particle cryogenic electron microscopy (cryo-EM) has enabled near-atomic resolution imaging of large macromolecules, enhancing functional insights. However, current cryo-EM refinement tools condense all single-particle images into a single structure, which can misrepresent highly flexible molecules like RNAs. Here, we combine molecular dynamics simulations with cryo-EM density maps to better account for the structural dynamics of a complex and biologically relevant RNA macromolecule. Namely, using metainference, a Bayesian method, we reconstruct an ensemble of structures of the group II intron ribozyme, which better match experimental data, and we reveal inaccuracies of single-structure approaches in modeling flexible regions. An analysis of all RNA-containing structures deposited in the PDB reveal that this issue affects most cryo-EM structures in the 2.5-4 A range. Thus, RNA structures determined by cryo-EM require careful handling, and our method may be broadly applicable to other RNA systems.
Glioblastoma Neurovascular Progenitor Orchestrates Tumor Cell Type Diversity
Authors: Fazzari Elisa , Azizad Daria J. , Yu Kwanha , Ge Weihong , Li Matthew X. , Nano Patricia R. , Kan Ryan L. , Tum Hong A. , Tse Christopher , Bayley Nicholas A. , Haka Vjola , Cadet Dimitri , Perryman Travis , Soto Jose A. , Wick Brittney , Raleigh David R. , Crouch Elizabeth E. , Patel Kunal S. , Liau Linda M. , Deneen Benjamin , Nathanson David A. , Bhaduri Aparna
Published: July 2024

Glioblastoma (GBM) is the deadliest form of primary brain tumor with limited treatment options. Recent studies have profiled GBM tumor heterogeneity, revealing numerous axes of variation that explain the molecular and spatial features of the tumor. Here, we seek to bridge descriptive characterization of GBM cell type heterogeneity with the functional role of individual populations within the tumor. Our lens leverages a gene program-centric meta-atlas of published transcriptomic studies to identify commonalities between diverse tumors and cell types in order to decipher the mechanisms that drive them. This approach led to the discovery of a tumor-derived stem cell population with mixed vascular and neural stem cell features, termed a neurovascular progenitor (NVP). Followingin situvalidation and molecular characterization of NVP cells in GBM patient samples, we characterized their functionin vivo.Genetic depletion of NVP cells resulted in altered tumor cell composition, fewer cycling cells, and extended survival, underscoring their critical functional role. Clonal analysis of primary patient tumors in a human organoid tumor transplantation system demonstrated that the NVP has dual potency, generating both neuronal and vascular tumor cells. Although NVP cells comprise a small fraction of the tumor, these clonal analyses demonstrated that they strongly contribute to the total number of cycling cells in the tumor and generate a defined subset of the whole tumor. This study represents a paradigm by which cell type-specific interrogation of tumor populations can be used to study functional heterogeneity and therapeutically targetable vulnerabilities of GBM.
Aberration correction in long GRIN lens-based microendoscopes for extended field-of-view two-photon imaging in deep brain regions
Authors: Sattin Andrea , Nardin Chiara , Daste Simon , Moroni Monica , Reddy Innem , Liberale Carlo , Panzeri Stefano , Fleischmann Alexander , Fellin Tommaso
Published: July 2024

Two-photon (2P) fluorescence imaging through gradient index (GRIN) lens-based endoscopes is fundamental to investigate the functional properties of neural populations in deep brain circuits. However, GRIN lenses have intrinsic optical aberrations, which severely degrade their imaging performance. GRIN aberrations decrease the signal-to-noise ratio (SNR) and spatial resolution of fluorescence signals, especially in lateral portions of the field-of-view (FOV), leading to restricted FOV and smaller number of recorded neurons. This is especially relevant for GRIN lenses of several millimeters in length, which are needed to reach the deeper regions of the rodent brain. We have previously demonstrated a novel method to enlarge the FOV and improve the spatial resolution of two-photon microendoscopes based on GRIN lenses of length < 4.1 mm (Antonini et al. eLife 2020). However, previously developed microendoscopes were too short to reach the most ventral regions of the mouse brain. In this study, we combined optical simulations with fabrication of aspherical polymer microlenses through three-dimensional (3D) microprinting to correct for optical aberrations in long (length > 6 mm) GRIN lens-based microendoscopes (diameter, 500 µm). Long corrected microendoscopes had improved spatial resolution, enabling imaging in significantly enlarged FOVs. Moreover, using synthetic calcium data we showed that aberration correction enabled detection of cells with higher SNR of fluorescent signals and decreased cross-contamination between neurons. Finally, we applied long corrected microendoscopes to perform large-scale and high precision recordings of calcium signals in populations of neurons in the olfactory cortex, a brain region laying approximately 5 mm from the brain surface, of awake head-tethered mice. Long corrected microendoscopes are powerful new tools enabling population imaging with unprecedented large FOV and high spatial resolution in the most ventral regions of the mouse brain.
Dual host-bacterial gene expression to study pathogenesis and the regulation of virulence factors in tissue during respiratory infections
Authors: Di Marco Federico , Nicola Francesca , Giannese Francesca , Saliu Fabio , Tonon Giovanni , de Pretis Stefano , Cirillo Daniela M. , Lorè Nicola I.
Published: July 2024

Co-localization of spatial transcriptome information of host and pathogen can revolutionize our understanding of microbial pathogenesis. Here, we aimed to demonstrate that customized bacterial probes can be successfully used to identify host-pathogen interactions in formalin-fixed-paraffin-embedded (FFPE) tissues by probe-based spatial transcriptomics technology. We analyzed the spatial gene expression of bacterial transcripts with the host transcriptomic profile in murine lung tissue chronically infected withMycobacterium abscessusembedded in agar beads. Customized mycobacterial probes were designed for the constitutively expressedrpoBgene (an RNA polymerase β subunit) and the virulence factor precursorlsr2, modulated by oxidative stress. We found a correlation between therpoBexpression, bacterial abundance in the airways, and an increased expression oflsr2virulence factor in lung tissue with high oxidative stress. Overall, we demonstrate the potential of dual bacterial and host gene expression assay in FFPE tissues, paving the way for the simultaneous detection of host and bacterial transcriptomes in pathological tissues.
CIB2 as a Ca2+Sensor for Auditory Mechano-Electrical Transduction and Linked to Genetic-Heterogeneity ofTMC1in Hearing Loss
Authors: Wu Shaoxuan , Lin Lin , Hu Qiaoyu , Yao Xuebo , Wang Hongyang , Liu Shuang , Liu Qingling , Xi Yuehui , Lin Yuzhe , Gong Jianqiao , Hu Ruixing , Zhan Wei , Luo Yi , He Guang , Liu Zhijun , Xiong Wei , Wang Qiuju , Xu Zhigang , Bai Fang , Lu Qing
Published: July 2024

Non-syndromic sensorineural hearing loss is characterized by genetic heterogeneity, leading to potential clinical misdiagnosis.TMC1, a unique causative gene associated with deafness, exhibits variants with autosomal dominant and recessive inheritance patterns.TMC1codes for the transmembrane channel-like 1 (TMC1), a key component of the mechano-electrical transduction (MET) machinery for hearing. However, the molecular mechanism of Ca2+regulation in MET, which is essential for sound perception, remains unclear. CIB2, another MET component associated with deafness, can bind with calcium and may play a role in MET gating. Our study reveals that the TMC1-CIB2 complex undergoes a Ca2+-induced conformational change, highlighting the crucial role of Ca2+in MET. We identified a vertebrate-specific binding site on TMC1, named CR3, that interacts withapoCIB2, with the binding interface linked to hearing loss. Using an in-vivo animal model, we demonstrated that disruption of the calcium-sensing site of CIB2 perturbs the MET channel conductivity, confirming its role as a Ca2+sensor for MET. Additionally, after systematically analyzing the hearing-loss variants, we observed that dominant mutations of TMC1 are often located near the ion pore or at the binding interfaces with the Ca2+sensor CIB2. This provides a detailed mechanism of the genetic heterogeneity ofTMC1in hearing loss at an atomic level.
Population genetics meets ecology: a guide to individual-based simulations in continuous landscapes
Authors: Chevy Elizabeth T. , Min Jiseon , Caudill Victoria , Champer Samuel E. , Haller Benjamin C. , Rehmann Clara T. , Smith Chris C. R. , Tittes Silas , Messer Philipp W. , Kern Andrew D. , Ramachandran Sohini , Ralph Peter L.
Published: July 2024

Individual-based simulation has become an increasingly crucial tool for many fields of population biology. However, continuous geography is important to many applications, and implementing realistic and stable simulations in continuous space presents a variety of difficulties, from modeling choices to computational efficiency. This paper aims to be a practical guide to spatial simulation, helping researchers to implement individual-based simulations and avoid common pitfalls. To do this, we delve into mechanisms of mating, reproduction, density-dependent feedback, and dispersal, all of which may vary across the landscape, discuss how these affect population dynamics, and describe how to parameterize simulations in convenient ways (for instance, to achieve a desired population density). We also demonstrate how to implement these models using the current version of the individual-based simulator, SLiM. We additionally discuss natural selection -- in particular, how genetic variation can affect demographic processes. Finally, we provide four short vignettes: simulations of pikas that shift their range up a mountain as temperatures rise; mosquitoes that live in rivers as juveniles and experience seasonally changing habitat; cane toads that expand across Australia, reaching 120 million individuals; and monarch butterflies whose populations are regulated by an explicitly modeled resource (milkweed).
Spatiotemporal dispersion of DENV1 genotype V in western Colombia
Authors: Rojas-Gallardo Diana , Ferrell Tyshawn , Escobar Paula , Lopez Diego , Giraldo Beatriz , Restrepo-Chica Juliana , Jimenez-Posada Erika , Martinez-Gutierrez Marlen , Ruiz-Sáenz Julian , Key Autum , Shariatzadeh Nima , Khosravi Dara , Martinez Megan A. , Bombin Andrei , Waggoner Jesse J. , Osorio Jorge E. , Neufeldt Christopher J , Collins Matthew H , Cardona-Ospina Jaime A. , Piantadosi Anne
Published: July 2024

Dengue virus (DENV) is a significant public health concern in Colombia, with increased transmission of DENV type 1 (DENV-1) in the departments of Risaralda and Valle del Cauca in the Central-West region of the country following a large outbreak in 2019. However, little is known about the source, genetic diversity, and evolution of circulating viruses. We obtained plasma samples from individuals with acute DENV infection and analyzed DENV-1 genetic diversity, phylodynamics, and phylogeography. We found that most viruses belonged to DENV-1 genotype V, and phylogenetic analysis revealed three distinct clades, each of which was most closely related to viruses from neighboring departments of Colombia sampled over the last 5-10 years. Thus, the 2019 outbreak and subsequent DENV-1 circulation was not due to the introduction of a new lineage but rather reflected local DENV-1V dispersion and evolution. We identified amino acid positions under positive selection in structural proteins and NS1, which may have a role in immune evasion and pathogenesis. Overall, our analysis of DENV1 genotype V diversity, evolution and spread within Colombia highlights the important role of genomic surveillance in understanding virus dynamics during endemic circulation and outbreaks.