bluuebunny/crossref_metadata_2025 huggingface dataset:
Employee perception of precision technology use at the dairy farm
Authors: Herrera Natalia , Vélez Juan , Holt Timothy , Pinedo Pablo
Published: March 2024

The adoption of precision technologies on dairy farms has increased significantly in recent decades, leading to the challenge of providing employees with resources to maximize the efficient use of these tools. The objective of this study was to explore how dairy farm employees perceive the available precision technologies and to identify possible challenges they face when adapting to their use at the farm. An online survey consisting of four sections (employee demographics, precision technologies in use, perception of these technologies, and opportunities for adapting to technology use) was completed from September to December 2022 by 266 farm employees from three dairies operated under similar management. Most of the respondents were identified as male (72.2%), Hispanic or Latino (92.5%), aged between 21 and 30 (39.1%) or 31 and 40 yr (36.8%), with a bachelor’s degree (34.6%) or completion of middle school (29.3%) and having basic or no English proficiency (74%). Overall, the respondents indicated being comfortable (95.6%) with and understanding (91.8%) the technology they use. Employees recognized precision technology as a tool that helps them to be more efficient (93.7%), identifying the technologies’ benefits (92.1%). However, challenges for adapting to these technologies included personal limitations, such as not knowing the language of the technology (31%), visual impairments (24%), light sensitivity (14%), and not being able to read (7%). Environmental limitations were also recognized and included cold weather (64.3%), wind (46%), and surroundings that were too dark (31%) or too bright (21%). Significant associations between perception of the technology and age, level of education, and English proficiency were identified. Respondents indicated their desire to learn more about precision technologies implemented at work, which could eventually lead to improved efficiency at the dairy operation through innovations in the way users interact with these technologies, increasing employees’ motivation. This study provides insights that could assist the dairy industry in addressing challenges and enhancing opportunities for a more efficient use of precision technologies at dairy farms.
A new amphibamiform from the Early Permian of Texas elucidates patterns of cranial diversity among terrestrial amphibamiforms
Authors: So Calvin , Pardo Jason D , Mann Arjan
Published: March 2024

Amphibamiform temnospondyls are at the forefront of discourse surrounding modern amphibian evolutionary origins. Here we present a new amphibamiform, Kermitops gratus gen. et sp. nov., from the Lower Clear Fork Formation of the Early Permian of Texas. Kermitops reveals a mosaic of features shared with other amphibamiforms and possesses unique characteristics, including an internarial fontanelle formed by the premaxillae without contribution of the nasals. It possibly possesses a basioccipital that contributes to the occipital condyle, which has significant implications for recent hypotheses of the evolution of the modern amphibian neurocranium. Parsimony analyses recover non-traditional amphibamiform relationships but place Kermitops within Amphibamiformes. Bayesian inference analysis captures a more traditional hypothesis of amphibamiform relationships; however, the time-calibrated analysis under the fossilized birth–death model recovers a topology that mirrors the parsimony topologies. The low robusticity of topologies across different permutations employing traditional and modern methods suggest a need for improvement of current morphological datasets of lissamphibian origins. A morphometric analysis of the crania of terrestrial amphibamiforms reveals the evolution of disparate cranial morphologies among coeval taxa from the Early Permian of Texas.
EGFR exon 18 delE709_T710insD mutated stage IV non-small cell lung cancer treated with osimertinib: a case report
Authors: Valcárcel Sena , Villanueva Noemi , Álvarez Carlos , Esteban Emilio
Published: March 2024

Mutations in tyrosine kinase domain of epidermal growth factor receptor (EGFR) are observed in approximately 15% of non-small cell lung cancer adenocarcinoma. Exon 19 deletions or exon 21 L858R mutations are predominant in frequency and show high sensitivity to EGFR tyrosine kinase inhibitors (TKIs). Exon 18 mutations are extremely rare and the delE709_T710insD mutation accounts for only 0.16% of mutations when occurring as a sole mutation. This specific mutation in exon 18 seems to respond to certain EGFR TKIs such as afatinib. However, given the rarity of this mutation, determining the most effective TKI for its treatment remains unclear. We report a 70-year-old woman diagnosed with stage IV-A lung adenocarcinoma harboring EGFR delE709_T710insD mutation treated in first-line with Osimertinib using standard schedule and doses experiencing renal toxicity and disease progression after 9 weeks of treatment.
Strategic Approaches for the Health Science Educator: Understanding Strategic Planning, Strategic Thinking, and Continuous Process Improvement and Their Impact
Authors: Lazarus Melanie M. , Bush Ruth L. , Perkowski Linda , McNeil Sara
Published: March 2024

With continued demand for health science institutions to find solutions to deliver on heightened student expectations despite smaller budgets and fewer resources, the utilization of organizational improvement techniques is pervasive. Academic health care leaders are seeking effective modalities to overcome obstacles, modernize, and become more efficient. Three of the commonly used approaches for improvement are strategic planning, strategic thinking, and continuous process improvement (CPI), and these concepts have been used in a variety of forms throughout industry, higher education, and health care. However, their definitions are often not well understood, and their processes are misconstrued in practice. With the increased expectation of health care institutions with undergraduate, graduate, and continuing education to consider strategic processes in organizational improvement, it is important for leadership to understand the differences in these three approaches. In this article, we explain the concepts of strategic planning, strategic thinking, and CPI through an overview of their history, definitions, and the benefits and pitfalls as observed by researchers. Furthermore, we reduce the noise in the existing literature into three concise definitions for each approach. And finally, for those seeking where to begin, we explain one tool in each category recommended for the novice strategist: the Strengths, Weaknesses, Opportunities, and Threats (SWOT) analysis for strategic planning, the Goals, Objectives, Strategies, and Tactics (GOST) framework for strategic thinking, and the Pareto Chart for CPI.
Preimplementation of Critical Care Early Mobility Clinical Decision Support
Authors: Dunn Heather , da Costa Ferreira Oberfrank Natany , Krupp Anna
Published: March 2024

Early mobility is a form of critical care rehabilitation ranging from in-bed exercise to ambulation and is known to limit post–intensive-care functional decline. Multiple barriers prevent widespread early mobility implementation. Clinical decision support systems can optimize the decision-making process and overcome barriers to care. However, critical care early mobility clinical decision support does not exist. Our objective was to develop and establish the content validation of the operational definitions for a novel critical care early mobility assessment instrument. Content validation was conducted in two steps: (1) development of operational definitions by the research team and (2) content validation with 10 nurse experts. Quality assessment and suitability of the operational definitions for 30 items, across four safety domains, were assessed using a 7 point-Likert scale. Item content validity index scores ranged from 0.6 to 0.1 after the first validation round. Domains containing items with item content validity index scores less than the lower limit of 0.78 were modified for clarity of language. Item content validity index scores ranged from 0.8 to 1.0, and the scale-level content validity index was 0.93 after the second content validation round. Excellent content validity of the operational definitions was achieved. This is the first methodological step in a larger project to develop clinical decision support for critical care early mobility.
Cocaine-Induced Plasma Cell Orificial “Dermatomucositis”: A More Accurate Descriptive Term for a Clearly Dermatological Entity
Authors: Fernandez-Flores Angel , González Montero José Manuel
Published: March 2024

Although the involvement of the nasal passages and nasal septum in cocaine users has been known for decades, a new presentation affecting the nostrils and upper lip with an inflamed appearance has recently been documented. The authors who identified this presentation termed it “cocaine-related plasma cell mucositis” due to the abundance of plasma cells in the infiltrate. In this article, we present a second case and emphasize the dermal involvement of the lip, leading us to consider the condition as a genuine dermatomucositis.
Qualitative Blade Topology in Donor Cornea Punches and Corresponding Endothelial Cell Loss in PK and DMEK Grafts
Authors: Straiko Megan M. W. , López Claudia S. , Hubbs Rebecca , Dye Phillip K. , Tran Khoa D.
Published: March 2024

Purpose:

Two commonly used donor cornea punches were assessed using quantification of peripheral endothelial cell loss (ECL) and scanning electron microscopy (SEM) of blade topology and associated features on donor grafts.

Methods:

Penetrating keratoplasty (PK) (n = 8 pairs) and Descemet membrane endothelial keratoplasty (DMEK) (n = 8 pairs) grafts were prepared from mate donor corneas using Moria Busin or Corza Barron donor cornea punches (all punches were 7.5 mm) and analyzed for global and peripheral ECL. Punches were examined by SEM and subsequently used to prepare PK grafts from mate donor corneas (n = 3 pairs) that were also assessed by SEM.

Results:

For PK grafts, peripheral ECL caused by Busin and Barron punches was 4.2% ± 0.6% and 4.0% ± 0.9% (P = 0.62), respectively. For DMEK grafts, peripheral ECL caused by Busin and Barron punches was 3.6% ± 1.9% and 3.0% ± 1.3% (P = 0.48), respectively. SEM analysis of the Busin punch identified a rolled blade with a seam; the Barron punch is created from full rod stock and is seamless. Busin punch PK grafts have a ridge of stromal tissue that was not observed in the Barron PK grafts. Both punches exhibit anomalies along the blade edge, and the stroma of both grafts exhibited “drag lines.”

Conclusions:

Both punches caused similar and minimal ECL. In PK grafts, the seam of the Busin punch may be the source of the observed uneven stromal surface. Striations and debris on the cutting surfaces of both punches may produce drag lines in cut stroma. These topological features may contribute to uneven donor–recipient tissue apposition, leading to astigmatism after PK.
Techniques in Nipple Areolar Reconstruction: A Retrospective Analysis of Surgical Interventions and Patient-reported Satisfaction Scores
Authors: Baker Nusaiba F. , Marxen Troy , Nguyen Jonathan , Danko Dora , Ebunlomo Tola , Carlson Grant W. , Thompson Peter W.
Published: March 2024

Background:

Nipple areolar complex (NAC) reconstruction often signifies completion of the breast reconstruction process for some patients and has been shown to improve both psychosocial and sexual well-being. Several techniques have been described; however, there currently exists little evidence in the literature describing outcomes or patient satisfaction.

Methods:

A retrospective analysis of NAC reconstructions over the last decade was queried for patient demographics, operative technique, and postoperative outcomes. A standardized, validated survey was also utilized to evaluate overall satisfaction, with a focus on aesthetic outcome, shape, color, and projection.

Results:

Eighty-three patients were identified, with 49 (59.0%) completing the survey. The modalities used for reconstruction include the C-V flap (45.7%), the modified skate flap technique (42.2%), and free nipple grafting (FNG, 12.0%). No significant differences in age, BMI, or comorbidities were found among the three types. The most utilized donor site for skate flap reconstruction was the suprapubic area (37.1%). There were also no significant differences in complication rate (C-V 10.5%, FNG 10%, skate 5.7%, P = 0.630) or revision surgery (C-V 2.6%, FNG 0%, skate 5.7%, P = 0.732). The most common complication was nipple necrosis. Adjusting for time to follow-up using multivariate analysis, there was a significant difference in overall patient satisfaction when compared across all three techniques, with the modified skate flap having the highest mean overall satisfaction scores.

Conclusions:

NAC reconstruction can be completed safely and effectively with a variety of techniques. The modified skate flap technique was associated with high levels of patient satisfaction and a low complication rate.
Treatment of Cicatricial Lower Eyelid Ectropion with Suture of Horner Muscle Combined with Fascia Transplantation
Authors: Takaya Kento , Sakai Shigeki , Kishi Kazuo
Published: March 2024

This case series aimed to describe a new technique for correcting contractures and deformities that reliably addresses lacrimal punctum deviation and severe cicatricial lower eyelid ectropion. This was a technical description and a retrospective interventional case series. Eyelid ectropion and lacrimal punctum deviation were treated surgically by grafting the fascia lata and suturing the tarsus-Horner muscle. In total, three patients underwent this surgery: one for burns, one for lower eyelid tumor resection, and the other for an orbital floor fracture following a motorcycle accident, all resulting in ectropion. All patients previously had failed ectropion correction procedures, including scar revision, skin grafting, auricular cartilage grafting, and lateral tarsal strips. The mean follow-up was 15.8 (12.5–18.5) months. Furthermore, all patients showed resolution of lower eyelid ectropion and significant improvement in lower eyelid contracture, with a mean increase of 4.0 (2.5–5) mm. No severe complications were observed, and they reported a significant improvement in ocular surface symptoms. Our study shows that tacking of the tarsus and Horner muscles in combination with fascia lata grafting is effective in correcting refractory cicatricial lower eyelid ectropion with deviation of the tear punctum.
Lead-associated mortality in the US 1999–2020: a time-stratified analysis of a national cohort
Authors: An De-Wei , Yu Yu-Ling , Hara Azusa , Martens Dries S. , Yang Wen-Yi , Cheng Yi-Bang , Huang Qi-Fang , Asayama Kei , Stolarz-Skrzypek Katarzyna , Rajzer Marek , Verhamme Peter , Nawrot Tim S. , Li Yan , Staessen Jan A.
Published: March 2024

Objectives:

We undertook time-stratified analyses of the National Health and Nutrition Examination Survey in the US to assess time trends (1999–2020) in the associations of blood lead (BL) with blood pressure, mortality, the BL-associated population attributable fraction (PAF).

Methods:

Vital status of participants, 20–79 years old at enrolment, was ascertained via the National Death Index. Regressions, mediation analyses and PAF were multivariable adjusted and standardized to 2020 US Census data.

Results:

In time-stratified analyses, BL decreased from 1.76 μg/dl in 1999–2004 to 0.93 μg/dl in 2017–2020, while the proportion of individuals with BL < 1 μg/dl increased from 19.2% to 63.0%. Total mortality was unrelated to BL (hazard ratio (HR) for a fourfold BL increment: 1.05 [95% confidence interval, CI: 0.93–1.17]). The HR for cardiovascular death was 1.44 (1.01–2.07) in the 1999–2000 cycle, but lost significance thereafter. BL was directly related to cardiovascular mortality, whereas the indirect BL pathway via BP was not significant. Low socioeconomic status (SES) was directly related to BL and cardiovascular mortality, but the indirect SES pathway via BL lost significance in 2007–2010. From 1999–2004 to 2017–2020, cardiovascular PAF decreased (P < 0.001) from 7.80% (0.17–14.4%) to 2.50% (0.05–4.68%) and number of lead-attributable cardiovascular deaths from 53 878 (1167–99 253) to 7539 (160–14 108).

Conclusion:

Due to implementation of strict environmental policies, lead exposure is no longer associated with total mortality, and the mildly increased cardiovascular mortality is not associated with blood lead via blood pressure in the United States.
Trauma- and Violence-Informed Empowering Care for Sexual Assault Survivors
Authors: Klein L. B. , Melnik Jessica , Curran Kimberly , Luebke Jeneile , Moore Kaylen M. , Ruiz Ashley M. , Brown Cassilynn , Parker Diara , Hernandez-White Isabel , Walsh Kate
Published: March 2024

Background

Forensic nurse examiners, including sexual assault nurse examiners, provide care for survivors holistically through healthcare, emotional support, connection to follow-up care, safety planning, and, if desired, evidence collection to aid in the prosecution of sexual assault. There is increasing recognition that trauma-informed care must also include an understanding of the impacts of structural violence on minoritized patients to ensure health equity.

Aim

To help address this guidance gap, we expanded Campbell and colleagues' empowering care model using a trauma- and violence-informed care (TVIC) lens.

Methods

We used an iterative discussion-based process that included five joint meetings between a seven-member transdisciplinary research team and a five-member nurse advisory board.

Results

In a TVIC-informed empowering care model, we propose behavioral examples for forensic nurses for each of Campbell et al.'s five key domains of empowering care for forensic nurse examinations (i.e., build rapport and establish trust, show compassion, provide patient-directed care, convey professionalism, and provide resource referral and follow-up).

Conclusions

These behavioral examples for nurses can help guide forensic nurse training and practice to reduce disparities in treatment and follow-up support. Structures and systems are needed that enable forensic nurses to provide trauma- and violence-informed empowering care to survivors of sexual assault and, over time, increase the accessibility of forensic nurse examinations and improve patient outcomes.
Workplace Productivity, Health and Wellbeing
Authors: Ojo Samson O. , Chater Angel M. , Hewson David J. , Bailey Daniel P.
Published: March 2024

Objective

The aim of the study was to evaluate the feasibility and potential effects of a workplace intervention to reduce and break up sitting.

Methods

Office workers were randomized in clusters to intervention (n = 22) or control (n = 22). The intervention included a height-adjustable workstation, education, computer prompt software, and line manager support. Outcomes included device-measured workplace sitting and ecological momentary assessed workplace productivity. Recruitment, retention, and data completion rates were assessed.

Results

Recruitment (N = 44), retention (91%), and workplace sitting measurement rates demonstrated study feasibility. At 8 weeks, workplace sitting was 11% lower (95% CI: −20.71, −1.30) in the intervention group compared with control participants. Intervention participants were also more engaged, motivated, and productive while sitting (P ≤ 0.016).

Conclusions

It was feasible to implement and evaluate this office workplace intervention, with potential benefits on workplace sitting and ecological momentary assessed productivity.
Nurses' Perceived Effects of Visitor Restrictions in Hospital Maternity Units
Authors: Iobst Stacey E. , Breman Rachel Blankstein , Black Hannah , Edmonds Joyce K.
Published: March 2024

Purpose:

To explore how perinatal nurses perceive the effects of visitor restrictions on patient care within a hospital setting.

Study Design and Methods:

We distributed a cross-sectional survey online to perinatal nurses in May of 2022. Characteristics of respondents were analyzed using descriptive statistics. Responses to an open-ended question were analyzed via conventional content analysis.

Results:

Among our sample of 101 nurses, we identified seven codes representing positive effects and seven codes representing negative effects. The most frequently reported positive effects were ability to provide person-centered care (n = 36, 35.6%) and less patient stress and more rest (n = 29, 28.7%). The most frequently reported negative effects were limited patient support (n = 22, 21.8%) and emotional distress to the patient (n = 15, 14.9%). Fourteen percent (n = 14) of respondents cited both positive and negative effects.

Clinical Implications:

Nurses perceived that visitor restrictions resulted in both positive and negative patient experiences. Balancing clinical needs and safety considerations with emotional needs of the childbearing individual requires careful consideration by maternity care clinicians and health care systems. Subsequent research is needed to determine optimal visitation policies during intrapartum and postpartum with consideration to hospital context and patient preferences for optimal care.
Back morphology and walking patterns mean 13.8 years after surgery for lumbar disk herniation in adolescents
Authors: Ruehr Livia , Blomé Sebastian , Kastrati Gránit , Lagerbäck Tobias , Jonsjö Martin , Möller Hans , Skorpil Mikael , Lasselin Julie , Lalouni Maria , Gerdhem Paul , Jensen Karin
Published: March 2024

Introduction:

In many pain conditions, there is lingering pain despite healed tissue damage. Our previous study shows that individuals who underwent surgery for lumbar disk herniation (LDH) during adolescence have worse health, more pain, and increased disk degeneration mean 13 years after surgery compared with controls. It is unclear if walking patterns segregate surgically treated LDH adolescents and controls at mean 13-year follow-up.

Objectives:

Here, we analyzed the relationship between gait, back morphology and other health outcomes in a cohort of individuals treated surgically because of lumbar disk herniation compared with controls.

Methods:

We analyzed gait during a walking paradigm, back morphology at the site of surgery, and standardized health outcomes, among individuals who received surgery for LDH as adolescents, “cases” (n = 23), compared with “controls” (n = 23).

Results:

There were gait differences in head (P = 0.021) and trunk angle (P = 0.021) between cases and controls in a direction where cases exhibited a posture associated with sickness. The gait variance was explained by subjective pain and exercise habits rather than objective disk degeneration.

Conclusion:

Over a decade after surgery for LDH during adolescence, health among cases is worse compared with controls. The head and trunk angles differ between cases and controls, indicating that the residual pain lingers and may cause changes in movement patterns long after a painful episode in early life. Gait may be a useful target for understanding maintenance of pain and disability among individuals treated surgically for LDH during adolescence.
Oleispirillum naphthae gen. nov., sp. nov., a bacterium isolated from oil sludge, and proposal of Oleispirillaceae fam. nov.
Authors: Peng Chenghui , Zhang Xue , Li Jiang , Yang Min , Ma Shichun , Fan Hui , Dai Lirong , Cheng Lei
Published: March 2024

A microaerophilic, Gram-negative, motile, and spiral-shaped bacterium, designated Y-M2T, was isolated from oil sludge of Shengli oil field. The optimal growth condition of strain Y-M2T was at 25 °C, pH 7.0, and in the absence of NaCl. The major polar lipid was phosphatidylethanolamine. The main cellular fatty acid was iso-C17  :  0 3-OH. It contained Q-9 and Q-10 as the predominant quinones. The DNA G+C content was 68.1 mol%. Strain Y-M2T showed the highest 16S rRNA gene sequence similarity to Telmatospirillum siberiense 26-4bT (91.1 %). Phylogenetic analyses based on 16S rRNA gene and genomes showed that strain Y-M2T formed a distinct cluster in the order Rhodospirillales. Genomic analysis showed that Y-M2T possesses a complete nitrogen-fixation cluster which is phylogenetically close to that of methanogene. The nif cluster, encompassing the nitrogenase genes, was found in every N2-fixing strain within the order Rhodospirillales. Phylogeny, phenotype, chemotaxonomy, and genomic results demonstrated that strain Y-M2T represents a novel species of a novel genus in a novel family Oleispirillaceae fam. nov. in the order Rhodospirillales, for which the name Oleispirillum naphthae gen. nov., sp. nov. was proposed. The type strain is Y-M2T (=CCAM 827T=JCM 34765T).
Gene expression reprogramming of Pseudomonas alloputida in response to arginine through the transcriptional regulator ArgR
Authors: Molina-Henares María Antonia , Ramos-González María Isabel , Rinaldo Serena , Espinosa-Urgel Manuel
Published: March 2024

Different bacteria change their life styles in response to specific amino acids. In Pseudomonas putida (now alloputida) KT2440, arginine acts both as an environmental and a metabolic indicator that modulates the turnover of the intracellular second messenger c-di-GMP, and expression of biofilm-related genes. The transcriptional regulator ArgR, belonging to the AraC/XylS family, is key for the physiological reprogramming in response to arginine, as it controls transport and metabolism of the amino acid. To further expand our knowledge on the roles of ArgR, a global transcriptomic analysis of KT2440 and a null argR mutant growing in the presence of arginine was carried out. Results indicate that this transcriptional regulator influences a variety of cellular functions beyond arginine metabolism and transport, thus widening its regulatory role. ArgR acts as positive or negative modulator of the expression of several metabolic routes and transport systems, respiratory chain and stress response elements, as well as biofilm-related functions. The partial overlap between the ArgR regulon and those corresponding to the global regulators RoxR and ANR is also discussed.
Factors associated with correct vaccination among children aged 24 to 48 months hospitalized in the national hospitals of Bujumbura
Authors: Niyongabo Felix , Butoyi Jean M. , Laetitia Niyoyunguruza , Esperance Kabusoni , Coppieters Yves
Published: March 2024

Introduction

In Africa, although vaccines are often available free of charge in health facilities, many children evade various strategies put in place to reach them. In recent years, despite Burundi maintaining high coverage in all antigens (over 80% since the launch of the PEV in 1980), performance has begun to decline. From 2015 to 2017, all coverage rates experienced a slight regression, and the WHO/UNICEF figures for 2018 confirm this downward trend. The objective of this work is to contribute to the reduction of infant morbidity and mortality due to vaccine-preventable diseases by identifying factors associated with correct vaccination among children aged 24 to 48 months hospitalized in national hospitals in Bujumbura.

Methodology

A cross-sectional analytical study was conducted in 4 national hospitals in Burundi. A sample of 216 children was selected, and the collected data were entered into Epinfo 7.2 software and transferred to Stata 15 for analysis. Three types of analyses were performed: descriptive analysis, univariate logistic regression, and multivariate logistic regression. After modeling, variables with a p-value <0.05 were considered associated with correct vaccination.

Results

Out of 216 children, correct vaccination was observed in 64.81%. The average age of mothers was 29.4 ± 5.43 years, ranging from 15 to 45 years. Factors significantly associated with correct vaccination after modeling were: husband’s level of education [OR = 15.41; P = 0.021], household income [OR = 10.23; P = 0.021], distance from residence to vaccination facility [OR = 0.12; P = 0.000], and mothers’ knowledge levels of vaccine-preventable diseases [OR = 1.73; P = 0.004]. The model was well-calibrated (the p-value of the Lemeshow test is 0.6697) with a 90% capacity to correctly classify observations.

Conclusion

The study’s results indicate that children are not properly vaccinated despite the service being free. Various factors influencing correct vaccination status were identified, including the level of education of the head of the household, income level, distance to vaccination facilities, and mothers’ knowledge of vaccine-preventable diseases. It is essential to implement interventions targeting these factors associated with correct vaccination to reduce morbidity and mortality from vaccine-preventable diseases.
A fatal case of peritonitis caused byDysgonomonas capnocytophagoidesharboring the novel metallo-beta-lactamase geneblaDYB-1
Authors: Imai Kazuo , Kodana Masahiro , Omachi Ryuha , Inoue Tsutomu , Okada Hirokazu , Maeda Takuya
Published: March 2024

Dysgonomonas capnocytophagoidesshows multidrug resistance to antibiotics and causes opportunistic infections in immunocompromised hosts. We report a fatal case of peritonitis caused byD. capnocytophagoidesin Japan. We identified a novel chromosomally encoded class B1 metallo-beta-lactamase gene designatedblaDYB-1and anermFSgene that contributed to multidrug resistance.
Quantitating SARS-CoV-2 Neutralizing Antibodies from Human Dried Blood Spots
Authors: Berman Katherine , Van Slyke Greta , Novak Hayley , Rock Jean M. , Bievenue Rachel , Damjanovic Amanda K. , DeRosa Kate L. , Mirabile Gianna , Girardin Roxie C. , Dupuis Alan P. , McDonough Kathleen A. , Parker Monica M. , Styer Linda M. , Mantis Nicholas J.
Published: March 2024

Background

In the earliest days of COVID-19 pandemic, the collection of dried blood spots (DBS) enabled public health laboratories to undertake population-scale seroprevalence studies to estimate rates of SARS-CoV-2 exposure. With SARS-CoV-2 seropositivity levels now estimated to exceed 94% in the United States, attention has turned to using DBS to assess functional (neutralizing) antibodies within cohorts of interest.

Methods

Contrived DBS eluates from convalescent, fully vaccinated and pre-COVID-19 serum samples were evaluated in SARS-CoV-2 plaque reduction neutralization titer (PRNT) assays, a SARS-CoV-2 specific 8-plex microsphere immunoassay, a cell-based pseudovirus assay, and two different spike-ACE2 inhibition assays, an in-house Luminex-based RBD-ACE2 inhibition assay and a commercial real-time PCR-based inhibition assay (NAB-Sure™).

Results

DBS eluates from convalescent individuals were compatible with the spike-ACE2 inhibition assays, but not cell-based pseudovirus assays or PRNT. However, the insensitivity of cell-based pseudovirus assays was overcome with DBS eluates from vaccinated individuals with high SARS-CoV-2 antibody titers.

Conclusion

SARS-CoV-2 neutralizing titers can be derived with confidence from DBS eluates, thereby opening the door to the use of these biospecimens for the analysis of vulnerable populations and normally hard to reach communities.
Autonomic Nervous System activity correlates with peak experiences induced by DMT and predicts increases in wellbeing
Authors: Bonnelle Valerie , Feilding Amanda , Rosas Fernando E. , Nutt David J. , Carhart-Harris Robin L. , Timmermann Christopher
Published: March 2024

Non-ordinary states of consciousness induced by psychedelics can be accompanied by so-called ‘peak experiences’, characterized at the emotional level by their intensity and positive valence. These experiences are strong predictors of positive outcomes following psychedelic-assisted therapy, and it is therefore important to better understand their biology. Despite growing evidence that the autonomic nervous system (ANS) plays an important role in mediating emotional experiences, its involvement in the psychedelic experience is poorly understood. The aim of this study was to investigate to what extant changes in the relative influence of the sympathetic (SNS) and parasympathetic nervous systems (PNS) over cardiac activity may reflect the subjective experience induced by the short-acting psychedelic N,N-Dimethyltryptamine (DMT). We derived measures of SNS and PNS activity from the electrocardiogram data of 17 participants (11 males, 6 females, mean age = 33.8 y, SD = 8.3) while they received either DMT or placebo. Results show that the joint influence of SNS and PNS (‘sympatho-vagal coactivation’) over cardiac activity was robustly correlated with participants ratings of ‘Spiritual Experience’ and ‘Insightfulness’ during the DMT experience, while also being related to improved wellbeing scores two weeks after the session. In addition, we found that the state of balance between the two ANS branches (‘sympatho-vagal balance’) before DMT injection predicted scores of ‘Insightfulness’ during the DMT experience. These findings demonstrate the important involvement of the ANS in psychedelic-induced peak experiences and may pave the way to the development of biofeedback-based tools to enhance psychedelic-therapy.

Significance statement

Psychedelics can give rise to intense positive subjective experiences - aligned with Maslow’s notion of ‘peak experiences’ - that can have a positive and enduring impact on mental health. Understanding how these experiences relate to peripheral physiology before and during the acute effects of psychedelics is an important object of enquiry, as it may help advance the therapeutic use of these compounds. In this study, we demonstrate that specific peripheral states computed from heart rate activity recordings predicted and correlated with acute peak experiences and increases in wellbeing. These findings have implications for the relationship between peripheral physiology and altered states of consciousness. Moreover, they highlight a putative marker of physiological ‘readiness’ prior the psychedelic experience that could predict therapeutically relevant mechanisms that might be modified to improve mental health outcomes in psychedelic-therapy.
Epigenetic and transcriptional consequences of chemically induced transposon mobilization in the endosperm
Authors: del Toro-de León Gerardo , van Boven Joram , Santos-González Juan , Jiao Wen-Biao , Schneeberger Korbinian , Köhler Claudia
Published: March 2024

Genomic imprinting, an epigenetic phenomenon leading to parent-of-origin-specific gene expression, has independently evolved in the endosperm of flowering plants and the placenta of mammals—tissues crucial for nurturing embryos. While transposable elements (TEs) frequently colocalize with imprinted genes and are implicated in imprinting establishment, direct investigations of the impact ofde novoTE transposition on genomic imprinting remain scarce. In this study, we explored the effects of chemically induced transposition of the Copia elementONSENon genomic imprinting inArabidopsis thaliana. Through the combination of chemical TE mobilization and doubled haploid induction, we generated a line with 40 newONSENcopies. Our findings reveal a preferential targeting of maternally expressed genes (MEGs) for transposition, aligning with the colocalization of H2A.Z and H3K27me3 in MEGs— both previously identified as promoters ofONSENinsertions. Additionally, we demonstrate that chemically-induced DNA hypomethylation induces global transcriptional deregulation in the endosperm, leading to the breakdown of MEG imprinting. This study provides insights into the consequences of chemically induced TE remobilization in the endosperm, underscoring the need for cautious interpretation of the connection between TEs and genomic imprinting.
Parallel Encoding of Speech in Human Frontal and Temporal Lobes
Authors: Hullett Patrick W. , Leonard Matthew K. , Gorno-Tempini Maria Luisa , Mandelli Maria Luisa , Chang Edward F.
Published: March 2024

Models of speech perception are centered around a hierarchy in which auditory representations in the thalamus propagate to primary auditory cortex, then to the lateral temporal cortex, and finally through dorsal and ventral pathways to sites in the frontal lobe. However, evidence for short latency speech responses and low-level spectrotemporal representations in frontal cortex raises the question of whether speech-evoked activity in frontal cortex strictly reflects downstream processing from lateral temporal cortex or whether there are direct parallel pathways from the thalamus or primary auditory cortex to the frontal lobe that supplement the traditional hierarchical architecture. Here, we used high-density direct cortical recordings, high-resolution diffusion tractography, and hemodynamic functional connectivity to evaluate for evidence of direct parallel inputs to frontal cortex from low-level areas. We found that neural populations in the frontal lobe show speech-evoked responses that are synchronous or occur earlier than responses in the lateral temporal cortex. These short latency frontal lobe neural populations encode spectrotemporal speech content indistinguishable from spectrotemporal encoding patterns observed in the lateral temporal lobe, suggesting parallel auditory speech representations reaching temporal and frontal cortex simultaneously. This is further supported by white matter tractography and functional connectivity patterns that connect the auditory nucleus of the thalamus (medial geniculate body) and the primary auditory cortex to the frontal lobe. Together, these results support the existence of a robust pathway of parallel inputs from low-level auditory areas to frontal lobe targets and illustrate long-range parallel architecture that works alongside the classical hierarchical speech network model.
Matrix alignment and density modulate YAP-mediated T-cell immune suppression
Authors: Sapudom Jiranuwat , Alatoom Aseel , Tipay Paul , Teo Jeremy CM
Published: March 2024

T-cells navigate through various mechanical environments within the body, adapting their behavior in response to these cues. An altered extracellular matrix (ECM) characterized by increased density and enhanced fibril alignment, as observed in cancer tissues, can significantly impact essential T-cell functions critical for immune responses. In this study, we used 3D collagen matrices with controlled density and fibril alignment to investigate T-cell migration, activation, and proliferation. Our results revealed that dense and aligned collagen matrices suppress T-cell activation through enhanced YAP signaling. By inhibiting YAP signaling, we demonstrated that T-cell activation within these challenging microenvironments improved, suggesting potential strategies to enhance the efficacy of immunotherapy by modulating T-cell responses in dense and aligned ECMs. Overall, our study deepens our understanding of T-cell mechanobiology within 3D relevant cellular microenvironments and provides insights into countering ECM-induced T-cell immunosuppression in diseases such as cancer.

Graphical abstract

Dense and aligned extracellular matrices suppress T-cell activation via YAP signaling, affecting immunotherapy efficacy in diseases such as cancer.
Defining phylogenetic relationships: a complete and minimal set of combinatorial properties for triplets
Authors: Valentin Rineau , Stéphane Prin
Published: March 2024

Triplets, as minimal informative rooted trees, are fundamental units of information in phylogenetics. Their importance for phylogenetic reconstruction, cladistic biogeography, or supertree methods relies on the fact that any rooted tree can be decomposed into a set of triplets. In order to formalize the tree building from a consistent triplet set, severalk-adic rules of inference, i.e., rules that allow us to deduce at least one new triplet from exactlykother ones, have been identified. However, it remains unclear whether it is possible to reduce all the possiblek-adic rules to a finite set of basic properties. In order to solve this problem, we propose here to define triplets in terms of degree of equivalence relations. Given the axiomatic definition of the latter, we establish a list of the most basic properties for triplets. With such an approach, we finally prove that the closure of any coherent triplet set can be computed uniquely from these basic properties.
Biodiversity impact of the consumption of peat and wood-fired district heating
Authors: Vainio Veera , El Geneidy Sami , Halme Panu , Peura Maiju , Kotiaho Janne S.
Published: March 2024

The use of biofuels is becoming an increasingly important part of national and corporate climate strategies. At the same time, the consumption-based biodiversity impacts of biofuels are generally poorly known. Here we used a consumption-based approach to assess the biodiversity impacts of peat and wood-fired district heating in Finland. We combined the information on the area of impacted ecosystems and their condition before and after the impact to evaluate the impact as habitat hectares, i.e., the loss in the condition of the impacted habitats. The habitat hectare approach has not been used in previous studies on consumption-based biodiversity impacts but could be replicated to assess biodiversity impacts in different contexts around the globe. We present an eight-step general protocol for such assessment and discuss the usability of the protocol in assessing consumption-based biodiversity impacts of district heating systems. Considering different fuel types, peat had the highest biodiversity impact per unit area, followed by chips from roundwood and logging residue chips. If we consider the impacts per unit energy, chips from roundwood had the highest and peat the lowest biodiversity impact. We conclude that it is possible to assess biodiversity impacts of raw material-based consumption, like we did in our example case. This protocol should be further developed and refined in different systems and with different raw materials.
Eye-movement artifact correction in infant EEG: A systematic comparison between ICA and Artifact Blocking
Authors: Srishyla Diksha , Webb Sara Jane , Elsabbagh Mayada , O’Reilly Christian ,   The BASIS Team
Published: March 2024

Background

Independent Component Analysis (ICA) is a well-established approach to clean EEG and remove the impact of signals of non-neural origin, such as those from muscular activity and eye movements. However, evidence suggests that ICA removes artifacts less effectively in infants than in adults. This study systematically compares ICA and Artifact Blocking (AB), an alternative approach proposed to improve eye-movement artifact correction in infant EEG.

Methods

We analyzed EEG collected from 50 infants between 6 and 18 months of age as part of the International Infant EEG Data Integration Platform (EEG-IP), a longitudinal multi-study dataset. EEG was recorded while infants sat on their caregivers’ laps and watched videos. We used ICA and AB to correct for eye-movement artifacts in the EEG and calculated the proportion of effectively corrected segments, signal-to-noise ratio (SNR), power-spectral density (PSD), and multiscale entropy (MSE) in manually selected EEG segments with and without eye-movement artifacts.

Results

On the one hand, the proportion of effectively corrected segments indicated that ICA corrected eye-movement artifacts (sensitivity) better than AB. SNR and PSD indicated that both AB and ICA correct eye-movement artifacts with equal sensitivity. MSE gave mixed results. On the other hand, AB caused less distortion to the clean segments (specificity) for SNR, PSD, and MSE.

Conclusions

Our results suggest that ICA is more sensitive (i.e., it better removes artifacts) but less specific (it distorts clean signals) than AB for correcting eye-movement artifacts in infant EEG.
Challenges in predicting PROTAC-mediated Protein-Protein Interfaces with AlphaFold
Authors: Pereira Gilberto P. , Gouzien Corentin , Souza Paulo C. T. , Martin Juliette
Published: March 2024

In the last few years, predicting the structure of PROTAC-mediated complexes emerged as a fundamental step toward the design of therapeutic modalities for cancer and other conditions. The development of AlphaFold2 (AF2) caused a paradigm shift in the structural biology community. From then onwards, further developments enabled the prediction of multimeric protein structures while improving calculation efficiency, leading to the widespread usage of AF2 and to the recent release of AF3. However, AF2 does not consider ligands, suggesting that ligand-mediated protein-protein interfaces (PPIs) are challenging to predict. One of the main claims of AF3 is that this limitation has been addressed, but the currently released webserver provides only a few ligands and no PROTACs are available. In this article, we benchmark the performance of AF2 on a test set of 28 PROTAC-mediated dimers, as well as a set of 326 protein hetero-dimers orthogonal to AF2 training set, with a special attention to the interface size and presence of ligand at the interface. We then evaluated whether the newly released AF3 model is able to outperform AF2 on the prediction of PROTAC-mediated complexes, despite not being able to include PROTAC ligands in the prediction. In this letter, we aimed at identifying possible reasons why AF-based methods fail to predict PROTAC-mediated interfaces. Our results show that AF2-multimer predictions are sensitive to the size of the interface to predict, with the majority of models being incorrect for the smallest interfaces. While it performs reasonably well for ligand-mediated interfaces in the absence of the ligand, AF2 is unable to predict PROTAC-mediated interfaces reliably. We also found that AF3 does not significantly improve upon the accuracy of AF2, as it is still unable to correctly predict PROTAC-mediated interfaces for the large majority of cases.
Impact of analytic decisions on test-retest reliability of individual and group estimates in functional magnetic resonance imaging: a multiverse analysis using the monetary incentive delay task
Authors: Demidenko Michael I. , Mumford Jeanette A. , Poldrack Russell A.
Published: March 2024

Empirical studies reporting low test-retest reliability of individual blood oxygen-level dependent (BOLD) signal estimates in functional magnetic resonance imaging (fMRI) data have resurrected interest among cognitive neuroscientists in methods that may improve reliability in fMRI. Over the last decade, several individual studies have reported that modeling decisions, such as smoothing, motion correction and contrast selection, may improve estimates of test-retest reliability of BOLD signal estimates. However, it remains an empirical question whether certain analytic decisionsconsistentlyimprove individual and group level reliability estimates in an fMRI task across multiple large, independent samples. This study used three independent samples (Ns: 60, 81, 119) that collected the same task (Monetary Incentive Delay task) across two runs and two sessions to evaluate the effects of analytic decisions on the individual (intraclass correlation coefficient [ICC(3,1)]) and group (Jaccard/Spearmanrho) reliability estimates of BOLD activity of task fMRI data. The analytic decisions in this study vary across four categories: smoothing kernel (five options), motion correction (four options), task parameterizing (three options) and task contrasts (four options), totaling 240 different pipeline permutations. Across all 240 pipelines, the median ICC estimates are consistently low, with a maximum median ICC estimate of .43 - .55 across the three samples. The analytic decisions with the greatest impact on the median ICC and group similarity estimates are theImplicit Baselinecontrast, Cue Model parameterization and a larger smoothing kernel. Using anImplicit Baselinein a contrast condition meaningfully increased group similarity and ICC estimates as compared to using theNeutralcue. This effect was largest for the Cue Model parameterization; however, improvements in reliability came at the cost of interpretability. This study illustrates that estimates of reliability in the MID task are consistently low and variable at small samples, and a higher test-retest reliability may not always improve interpretability of the estimated BOLD signal.