bluuebunny/crossref_metadata_2025 huggingface dataset:
A case report of isolated arrhythmogenic left ventricular cardiomyopathy: phenotypes, diagnosis, and treatment
Authors: Lan Yang , Wei Lai , Pan Cuizhen , Lin Tzuchun , Yan Yan
Published: February 2024

Background

Isolated arrhythmogenic left ventricular cardiomyopathy (IALVC) is a hereditary cardiomyopathy that is characterized by the replacement of left ventricular (LV) cardiomyocytes with fibrous and adipose tissue.

Case summary

A 55-year-old male patient presented with recurrent chest pain and palpitations characterized by episodes of monomorphic ventricular tachycardia and T-wave inversion. Coronary angiography was conducted to rule out myocardial ischaemia as the cause of chest pain. Echocardiography results revealed ventricular aneurysm formation at the apex of the left ventricle. Structural alterations of the cardiac magnetic resonance were consistent with the diagnosis of arrhythmogenic left ventricular cardiomyopathy with LV alterations without right ventricular involvement. Pathological staining of the lesion area further confirmed the diagnosis of IALVC. The TTN1 c.17617 C>A mutation in arrhythmogenic cardiomyopathy was identified using whole exome sequencing. His symptoms improved by the treatments including implantable cardioverter defibrillator (ICD) implantation, radiofrequency ablation, and ventricular aneurysm resection.

Discussion

The patient presented with IALVC with apical fibrofatty displacement and underwent surgical management, highlighting the importance of multimodal imaging, gene analysis, and histopathological findings for timely diagnosis, and emphasizing the benefits of life-saving therapy, including ICD implantation, radiofrequency ablation, and ventricular aneurysm resection. These findings contribute to a deeper understanding of the clinical presentation and outcome of IALVC.
Intraoperative indocyanine green imaging as an adjunctive technique to reduce any circumflex artery damage during mitral valve surgery: a feasibility study
Authors: Savini Carlo , Costantino Antonino , Fiorentino Mariafrancesca , Zucchetta Fabio , Cavallucci Andrea , Mikus Elisa
Published: February 2024

Iatrogenic injuries to the circumflex coronary artery during mitral valve surgery are probably underestimated (reported rates of 0.3–1.8%). This complication arises from the artery's close proximity to the mitral annulus, particularly at the anterolateral commissure. The study aimed to assess this risk in a patient group prone to such injury. The surgical procedure utilized a minimally invasive approach and indocyanine green-based fluorescence imaging. This technique allows a real-time visualization of the circumflex artery, aiding precise placement of annular sutures and minimizing the risk of injury. The method, applied in 6 patients, integrates preoperative assessments with intraoperative fluorescence imaging, ensuring accurate arterial depiction and preventing iatrogenic damage. The study highlights the safety and efficacy of fluorescence imaging, especially in identifying vessel anomalies, indicating potential applications in various cardiac procedures.
Small dense low-density lipoprotein cholesterol and coronary artery calcification in the Multi-Ethnic Study of Atherosclerosis
Authors: Rikhi Rishi , Schaich Christopher L , Hafzalla George W , Patel Nisha A , Tannenbaum Jordan E , German Charles A , Polonsky Tamar , Tsai Michael Y , Ahmad Muhammad Imtiaz , Islam Tareq , Chevli Parag A , Shapiro Michael D
Published: February 2024

Aims

Elevated small dense LDL cholesterol (sd-LDL-C) increases atherosclerotic cardiovascular disease (CVD) risk. Although coronary artery calcification (CAC) is widely used for predicting CVD events, few studies have examined the relationship between sd-LDL-C and CAC.

Methods and results

This study included 4672 individuals with directly measured baseline sd-LDL-C and CAC from the Multi-Ethnic Study of Atherosclerosis [mean (standard deviation) age: 61.9 (10.4) years; 52.5% women; 47.3% with baseline CAC (mean score >0)]. We used multi-variable general linear models and restricted cubic splines with the goodness of fit testing to evaluate the association of sd-LDL-C with the presence of CAC. Odds ratios [OR (95% confidence interval)] were adjusted for demographics and cardiovascular risk factors, including estimated total LDL-C. Higher quartiles of sd-LDL-C were associated with the presence of CAC, even after accounting for total LDL-C. Compared with the lowest quartile of sd-LDL-C, participants in Quartiles 2, 3, and 4 had higher odds for the presence of baseline CAC [Quartile 2 OR: 1.24 (1.00, 1.53); Quartile 3 OR: 1.51 (1.19, 1.93); and Quartile 4 OR 1.59 (1.17, 2.16)]. Splines suggested a quadratic curvilinear relationship of continuous sd-LDL-C with CAC after adjustment for demographics and CVD risk factors (quadratic vs. first-order sd-LDL-C terms likelihood ratio test: P = 0.015), but not after accounting for total LDL-C (quadratic vs. first-order terms: P = 0.156).

Conclusion

In a large, multi-ethnic sample without known CVD, higher sd-LDL-C was associated with the presence of CAC, above and beyond total LDL-C. Whether selective direct measurement of sd-LDL-C is indicated to refine cardiovascular risk assessment in primary prevention warrants further investigation.
Successful outpatient parenteral antibiotic therapy with cefiderocol for osteomyelitis caused by multi-drug resistant Gram-negative bacteria: a case report
Authors: Schellong Paul , Wennek-Klose Janett , Spiegel Christian , Rödel Jürgen , Hagel Stefan
Published: February 2024

Objectives

Post-traumatic osteomyelitis attributed to metallo-β-lactamase (MBL)-producing Gram-negative bacteria presents a challenging clinical scenario. Cefiderocol emerges as a viable treatment option within the limited therapeutic options available.

Patient/case description

In this brief report, we present a case of a Ukrainian patient with osteomyelitis caused by multi-drug resistant Pseudomonas aeruginosa, which was successfully treated with cefiderocol, facilitated in part by outpatient parenteral antibiotic therapy (OPAT).

Results and discussion

Administration of Cefiderocol via OPAT can present a safe and effective option for treatment of post-traumatic osteomyelitis with multi-drug resistant Pseudomonas aeruginosa. A possible effect on iron homeostasis of extended treatment duration with cefiderocol may be taken into consideration.
Round-up of fashion-related IP decisions 2023
Authors:   The Bird & Bird IP Team, Mestroni Shariqa , Wijesena Shehana , Lewis Lynne , Švecová Denisa , Lexman-nová Karin , Gustafsson Amalie , Baun Emilie , Arbant Géraldine , Vrhovac Pava , Grundmann Mascha , Präger Julia , Andreotta Cristiana , Massalongo Sara , Rombolá Francesca , Dorenbosch Nina , Kostrzewa Julia , Żuk Mateusz , Cueto Antonio , Danos Christine , Hughes Ciara , Naia Alessandra
Published: February 2024

In 2023, courts and competent authorities in Australia, Czech Republic, Denmark, France, Germany, Italy, the Netherlands, Poland, Spain and the United Kingdom delivered a series of important rulings of interest to and affecting the fashion sector. This contribution provides a round-up of the most significant fashion-related IP judgments issued in the period 1 January to 31 December 2023. The analysis is organized by substantive IP right and enforcement aspects, and is organized by country.
SumoPred-PLM: human SUMOylation and SUMO2/3 sites Prediction using Pre-trained Protein Language Model
Authors: Palacios Andrew Vargas , Acharya Pujan , Peidl Anthony Stephen , Beck Moriah Rene , Blanco Eduardo , Mishra Avdesh , Bawa-Khalfe Tasneem , Pakhrin Subash Chandra
Published: February 2024

SUMOylation is an essential post-translational modification system with the ability to regulate nearly all aspects of cellular physiology. Three major paralogues SUMO1, SUMO2 and SUMO3 form a covalent bond between the small ubiquitin-like modifier with lysine residues at consensus sites in protein substrates. Biochemical studies continue to identify unique biological functions for protein targets conjugated to SUMO1 versus the highly homologous SUMO2 and SUMO3 paralogues. Yet, the field has failed to harness contemporary AI approaches including pre-trained protein language models to fully expand and/or recognize the SUMOylated proteome. Herein, we present a novel, deep learning-based approach called SumoPred-PLM for human SUMOylation prediction with sensitivity, specificity, Matthew's correlation coefficient, and accuracy of 74.64%, 73.36%, 0.48% and 74.00%, respectively, on the CPLM 4.0 independent test dataset. In addition, this novel platform uses contextualized embeddings obtained from a pre-trained protein language model, ProtT5-XL-UniRef50 to identify SUMO2/3-specific conjugation sites. The results demonstrate that SumoPred-PLM is a powerful and unique computational tool to predict SUMOylation sites in proteins and accelerate discovery.
Bridging digital and electromagnetic realms for enhanced wireless communication: current space
Authors: Abbasi Qammer H
Published: February 2024

Recently, Tie Jun Cui and team members introduced innovative macroscopic and statistical models for digital coding metasurfaces, bridging the digital and electromagnetic realms and quantifying information loss for enhanced wireless communication system design. This is a highlight of it.
Displacement-pressure biparametrically regulated softness sensory system for intraocular pressure monitoring
Authors: Cheng Yu , Zhan Yifei , Guan Fangyi , Shi Junli , Wang Jingxiao , Sun Yi , Zubair Muhammad , Yu Cunjiang , Guo Chuan Fei
Published: February 2024

High intraocular pressure (IOP) is one of the high-risk pathogenic factors of glaucoma. Existing methods of IOP measurement are based on the direct interaction with the cornea. Commercial ophthalmic tonometers based on snapshot measurements are expensive, bulky, and their operation requires trained personnel. Theranostic contact lenses are easy to use, but they may block vision and cause infection. Here, we report a sensory system for IOP assessment that uses a soft indentor with two asymmetrically deployed iontronic flexible pressure sensors to interact with the eyelid-eyeball in an eye-closed situation. Inspired by human fingertip assessment of softness, the sensory system extracts displacement-pressure information for soft evaluation, achieving high accuracy IOP monitoring (>96%). We further design and custom-make a portable and wearable ophthalmic tonometer based on the sensory system and demonstrate its high efficacy in IOP screening. This sensory system paves a way towards cost-effective, robust, and reliable IOP monitoring.
Toward Nuclear Physics from Lattice QCD on Quantum Computers
Authors: Yamamoto Arata , Doi Takumi
Published: February 2024

One of the ultimate missions of lattice quantum chromodynamics (QCD) is to simulate atomic nuclei from the first principles of the strong interaction. This is an extremely hard task for current computational technology, but might be reachable in the coming quantum computing era. In this paper, we discuss the computational complexities of classical and quantum simulations of lattice QCD. It is shown that the quantum simulation scales better as a function of nucleon number and thus will outperform classical simulation for large nuclei.
Oxidative stress in metabolic dysfunction‐associated steatotic liver disease (MASLD): How does the animal model resemble human disease?
Authors: Jakubek Patrycja , Kalinowski Piotr , Karkucinska‐Wieckowska Agnieszka , Kaikini Aakruti , Simões Inês C. M. , Potes Yaiza , Kruk Beata , Grajkowska Wieslawa , Pinton Paolo , Milkiewicz Piotr , Grąt Michał , Pronicki Maciej , Lebiedzinska‐Arciszewska Magdalena , Krawczyk Marcin , Wieckowski Mariusz R.
Published: February 2024

Despite decades of research, the pathogenesis of metabolic dysfunction‐associated steatotic liver disease (MASLD) is still not completely understood. Based on the evidence from preclinical models, one of the factors proposed as a main driver of disease development is oxidative stress. This study aimed to search for the resemblance between the profiles of oxidative stress and antioxidant defense in the animal model of MASLD and the group of MASLD patients. C57BL/6J mice were fed with the Western diet for up to 24 weeks and served as the animal model of MASLD. The antioxidant profile of mice hepatic tissue was determined by liquid chromatography‐MS3 spectrometry (LC–MS/MS). The human cohort consisted of 20 patients, who underwent bariatric surgery, and 6 controls. Based on histological analysis, 4 bariatric patients did not have liver steatosis and as such were also classified as controls. Total antioxidant activity was measured in sera and liver biopsy samples. The hepatic levels of antioxidant enzymes and oxidative damage were determined by Western Blot. The levels of antioxidant enzymes were significantly altered in the hepatic tissue of mice with MASLD. In contrast, there were no significant changes in the antioxidant profile of hepatic tissue of MASLD patients, except for the decreased level of carbonylated proteins. Decreased protein carbonylation together with significant correlations between the thioredoxin system and parameters describing metabolic health suggest alterations in the thiol‐redox signaling. Altogether, these data show that even though the phenotype of mice closely resembles human MASLD, the animal‐to‐human translation of cellular and molecular processes such as oxidative stress may be more challenging.
Cognitive and Cerebrospinal Fluid Alzheimer’s Disease–related Biomarker Trajectories in Older Surgical Patients and Matched Nonsurgical Controls
Authors: Reese Melody , Wong Megan K. , Cheong Vanessa , Ha Christine I. , Cooter Wright Mary , Browndyke Jeffrey , Moretti Eugene , Devinney Michael J. , Habib Ashraf S. , Moul Judd W. , Shaw Leslie M. , Waligorska Teresa , Whitson Heather E. , Cohen Harvey J. , Welsh-Bohmer Kathleen A. , Plassman Brenda L. , Mathew Joseph P. , Berger Miles ,   the Markers of Alzheimer’s Disease and neuroCognitive Outcomes after Perioperative Care (MADCO-PC) Investigators
Published: February 2024

Background

Anesthesia and/or surgery accelerate Alzheimer’s disease pathology and cause memory deficits in animal models, yet there is a lack of prospective data comparing cerebrospinal fluid (CSF) Alzheimer’s disease–related biomarker and cognitive trajectories in older adults who underwent surgery versus those who have not. Thus, the objective here was to better understand whether anesthesia and/or surgery contribute to cognitive decline or an acceleration of Alzheimer’s disease–related pathology in older adults.

Methods

The authors enrolled 140 patients 60 yr or older undergoing major nonneurologic surgery and 51 nonsurgical controls via strata-based matching on age, sex, and years of education. CSF amyloid β (Aβ) 42, tau, and p-tau-181p levels and cognitive function were measured before and after surgery, and at the same time intervals in controls.

Results

The groups were well matched on 25 of 31 baseline characteristics. There was no effect of group or interaction of group by time for baseline to 24-hr or 6-week postoperative changes in CSF Aβ, tau, or p-tau levels, or tau/Aβ or p-tau/Aβ ratios (Bonferroni P > 0.05 for all) and no difference between groups in these CSF markers at 1 yr (P > 0.05 for all). Nonsurgical controls did not differ from surgical patients in baseline cognition (mean difference, 0.19 [95% CI, –0.06 to 0.43]; P = 0.132), yet had greater cognitive decline than the surgical patients 1 yr later (β, –0.31 [95% CI, –0.45 to –0.17]; P < 0.001) even when controlling for baseline differences between groups. However, there was no difference between nonsurgical and surgical groups in 1-yr postoperative cognitive change in models that used imputation or inverse probability weighting for cognitive data to account for loss to follow up.

Conclusions

During a 1-yr time period, as compared to matched nonsurgical controls, the study found no evidence that older patients who underwent anesthesia and noncardiac, nonneurologic surgery had accelerated CSF Alzheimer’s disease–related biomarker (tau, p-tau, and Aβ) changes or greater cognitive decline.

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Unveiling the Rare Presentation of Acetylsalicylate Overdose: Grand Round
Authors: Kohara Saeko , Kamijo Yoshito , Kyan Ryoko , Hishikawa Tsuyoshi , Okada Ichiro , Hasegawa Eiju
Published: February 2024

Background:

This case report highlights a rare occurrence of aspirin overdose presenting only as severe coagulopathy.

Case presentation:

An 85-year-old woman was admitted to the hospital with multiple lumbar vertebral compression fractures causing severe back pain. The patient had self-medicated with excessive consumption of Bufferin A containing 330 mg of aspirin. On arrival, she showed no typical symptoms of salicylate toxicity, such as nausea, vomiting, hyperventilation, tinnitus, or hearing loss. However, blood work revealed a significant decrease in vitamin K–dependent coagulation factors leading to coagulopathy. The administration of 20-mg menatetrenone (vitamin K) resulted in rapid improvement in coagulation abnormalities. The patient's blood salicylate level was later determined to be 42.7 mg/dL.

Discussion:

Acute salicylate poisoning is known to cause coagulopathy because of the inhibition of vitamin K–dependent coagulation factors. However, this case is unique because it demonstrates coagulopathy as the sole manifestation of aspirin toxicity without any other symptoms.

Conclusions:

This case highlights the importance of considering the possibility of aspirin toxicity in patients with coagulopathy, especially those who are regularly consuming aspirin.
ECMOve: A Mobilization Device for Extracorporeal Membrane Oxygenation Patients
Authors: van Galen Danny J. M. , Meinders Quint , Halfwerk Frank R. , Arens Jutta
Published: February 2024

Extracorporeal membrane oxygenation (ECMO) is a temporary lifesaving treatment for critically ill patients with severe respiratory or cardiac failure. Studies demonstrated the feasibility of in-hospital mobilizing during and after ECMO treatment preventing neuromuscular weakness and impaired physical functioning. Despite more compact mobile ECMO devices, implementation of ambulatory ECMO remains labor-intensive, complex, and challenging. It requires a large multidisciplinary team to carry equipment, monitor and physically support the patient, and to provide a back-up wheelchair in case of fatigue. Moreover, there is no adequate solution to ensure the stability of the patient’s cannula and circuit management during ambulation. We developed a system contributing to improvement and innovation of current ambulatory ECMO patient programs. Our modular cart-in-cart system carries necessary ECMO equipment, features an extendable walking frame, and contains a folding seat for patient transport. An adjustable shoulder brace with lockable tubing-connectors enables safe fixation of the blood tubing. ECMOve provides safety, support, and accessibility while performing ambulatory ECMO for both patient and caregiver. Prototype evaluation in a simulated intensive care unit showed feasibility of our design, but needs to be evaluated in clinical care.
Effective factors of severity of traffic accident traumas based on the Haddon matrix: a systematic review and meta-analysis
Authors: Golfiroozi Saeed , Nikbakht Hossein-Ali , Fahim Yegane Seyede Almas , Gholami Gharab Saeed , Shojaie Layla , Ahmad Hosseini Seyed , Rajabi Abdolhalim , Ghelichi-Ghojogh Mousa
Published: February 2024

Objective:

This study aims to investigate the factors affecting the severity of trauma caused by traffic accidents based on martrix Haddon; a systematic review and meta-analysis.

Methods:

In this study searched five international databases in this study, including Medline/PubMed, ProQuest, Scopus, Web of Knowledge, and Google Scholar, for published articles by the end of 2022. Data were entered into the statistical program and analyses were performed using STATA 17.0 software. Odds ratio (OR) values were computed for severity accidents.

Results:

Results of study showed that among the risk factors related to the host, not using helmet increased the risk of injury severity by 3.44 times compared to people who have used helmets (OR Not using helmet/Using helmet = 3.44, 95% CI: 2.27–5.00, P=0.001, I2=0.00%). Also, crossing over a centre divider has a protective role for the risk of injury severity compared to undertaking (OR crossing over a centre divider/undertaking=0.39, 95% CI: 0.20–0.75, P=0.01, I2=25.79%). in terms of the type of accident, accident of car-car reduces the risk of injury severity by 23% compared to accident of car-pedestrian (OR accident of car-car/accident of car-pedestrian=0.77, 95% CI: 0.61–0.96, P=0.02, I2=0.00%).

Conclusions:

It is necessary to pay attention to the intersection of human, vehicle and environmental risks and their contribution and how they interact. Based on the Haddon matrix approach, special strategies can be designed to prevent road damage. Safety standards for vehicles should also be addressed through stricter legal requirements and inspections.
Sudden Death Due to Rupture of Aneurysm of Sinus Valsalva: An Autopsy Case
Authors: Temel Dağ Merve , Buğra Aytül , Buğra Abdul Kerim
Published: February 2024

Aneurysm of sinus Valsalva is a defined as dilatation of the sinuses located between the aortic valve annulus and the sinotubular junction and mostly found in the right coronary sinus. It can be either congenital or acquired. This condition is usually asymptomatic unless it can cause intracardiac rupture or aortic valve insufficiency. Extracardiac rupture and associated fatal cases of cardiac tamponade are extremely rare. Our case is one of the rare cases in the literature that was diagnosed during autopsy. Our case is 65-year-old male patient with a history of hypertension suddenly fell ill after swimming in the sea. On gross examination of heart, there was an aneurysmatic enlargement of the right sinus Valsalva measuring 4.5 × 4 cm with a hemorrhagic appearance on the outer surface and a 0.3 cm rupture area. Histopathological examination revealed hemorrhage in and around the aneurysm wall.
A Novel Serum Exosomal miRNA Signature in the Early Prediction of Persistent Organ Failure in Patients with Acute Pancreatitis
Authors: Li Lei , Zhang Qichen , Feng Yongpu , Kong Fanyang , Sun Fengyuan , Xie Pei , Zhao Jiangman , Yu Hang , Zhou Jiahuan , Wu Shouxin , Zhao Shengbing , Li Zhaoshen , Liu Feng , Du Yiqi , Kong Xiangyu
Published: February 2024

Objective:

Current study aims to investigate whether serum exosomal microRNAs (miRNAs) could be potential biomarkers in predicting APs with POF at early phase.

Background:

Novel biomarkers are sorely needed for early prediction of persistent organ failure (POF) in acute pancreatitis (AP) patients.

Methods:

In the discovery stage, exosomal miRNAs were profiled in sera from APs with or without POF (5 vs. 5) using microarrays. POF-associated miRNA signatures then were assessed in training cohort (n=227) and further validated in three independent cohorts (n=516), including one nested case-control cohort.

Results:

A total of 743 APs were recruited in this large-scale biomarker identification study with a nested case-control study. Data from the discovery cohort demonstrated that 90 exosomal miRNAs were significantly dysregulated in APs with POF compared with controls. One miRNA classifier (Cmi) comprising 3 miRNAs (miR-4265, 1208, 3127-5p) was identified in the training cohort, and was further evaluated in two validation cohorts for their predictive value for POF. AUCs for Cmi ranged from 0.88 to 0.90, which was statistically superior to AUCs of APACHE-II and BISAP, and outperformed BUN and creatinine in POF prediction across all cohorts (P<.05). Higher levels of Cmi indicated increased need for ICU admission, prolonged hospitalization, and elevated mortality rate, thus poor prognosis. In the nested case-control study, Cmi could help identify prediagnostic POF in post-ERCP pancreatitis cases within “golden hours” after ERCP with high efficacy.

Conclusions:

Serum exosomal Cmi may be an early predictor for POF in AP, even within “golden hours” after AP onset.

Trial registration:

ClinicalTrials.gov (NCT02602808)
Multi-parametric optimization for controlling bifurcation structures
Authors: Mélot A. , Denimal E. , Renson L.
Published: February 2024

Bifurcations organize the dynamics of many natural and engineered systems. They induce qualitative and quantitative changes to a system’s dynamics, which can have catastrophic consequences if ignored during design. In this paper, we propose a general computational method to control the local bifurcations of dynamical systems by optimizing design parameters. We define an objective functional that enforces the appearance of local bifurcation points at targeted locations or even encourages their disappearance. The methodology is an efficient alternative to bifurcation tracking techniques capable of handling many design parameters (

>

10
2

). The method is demonstrated on a Duffing oscillator featuring a hardening cubic nonlinearity and an autonomous van der Pol-Duffing oscillator coupled to a nonlinear tuned vibration absorber. The finite-element model of a clamped-free Euler–Bernoulli beam, coupled with a reduced-order modelling technique, is also used to show the extension to the shape optimization of more complicated structures. Results demonstrate that several local bifurcations of various types can be handled simultaneously by the bifurcation control framework, with both parameter and state target values.
Threshold shifts and developmental temperature impact trade-offs between tolerance and plasticity
Authors: van Heerwaarden Belinda , Sgrò Carla , Kellermann Vanessa M.
Published: February 2024

Mounting evidence suggests that ectotherms are already living close to their upper physiological thermal limits. Phenotypic plasticity has been proposed to reduce the impact of climate change in the short-term providing time for adaptation, but the tolerance-plasticity trade-off hypothesis predicts organisms with higher tolerance have lower plasticity. Empirical evidence is mixed, which may be driven by methodological issues such as statistical artefacts, nonlinear reaction norms, threshold shifts or selection. Here, we examine whether threshold shifts (organisms with higher tolerance require stronger treatments to induce maximum plastic responses) influence tolerance-plasticity trade-offs in hardening capacity for desiccation tolerance and critical thermal maximum (CTMAX) acrossDrosophilaspecies with varying distributions/sensitivity to desiccation/heat stress. We found evidence for threshold shifts in both traits; species with higher heat/desiccation tolerance required longer hardening treatments to induce maximum hardening responses. Species with higher heat tolerance also showed reductions in hardening capacity at higher developmental acclimation temperatures. Trade-off patterns differed depending on the hardening treatment used and the developmental temperature flies were exposed to. Based on these findings, studies that do not consider threshold shifts, or that estimate plasticity under a narrow set of environments, will have a limited ability to assess trade-off patterns and differences in plasticity across species/populations more broadly.
Solibacillus palustris sp. nov., isolated from wetland soil of ecology park
Authors: Jo Jung-Hun , Lee Soon-Youl , Rhee Moon-Soo , Lee Kang-Hyun , Chun Se-Yoon , Im Wan-Taek
Published: February 2024

A Gram-staining-positive, motile, aerobic and rod-shaped bacterium, designated strain MA9T was isolated from wetland soil of ecology park, in Seoul, Republic of Korea. This bacterium was characterized to determine its taxonomic position by using the polyphasic approach. Strain MA9T grew at 10–37 °C and at pH 6.0–9.5 on TSB. Menaquinone MK-7 was the predominant respiratory quinone and iso-C15 : 0, iso-C16 : 0 and C16 : 1
 ω7c alcohol were the major fatty acids. The main polar lipids were phosphatidylethanolamine (PE), phosphatidylserine (PS), diphosphatidylglycerol (DPG) and phosphatidylglycerol (PG). The peptidoglycan type of the cell wall was A4α l-Lys-d-Glu. Based on 16S rRNA gene sequencing, strain MA9T clustered with species of the genus Solibacillus and appeared closely related to S. silvestris DSM 12223T (97.8 % sequence similarity), S. cecembensis DSM 21993T (97.6 %), S. isronensis DSM 21046T (97.6 %) and S. kalamii DSM 101595T (96.6 %). The G+C content of the genomic DNA was 37.0 mol%. Digital DNA–DNA hybridization between strain MA9T and type strains of S. silvestris, S. isronensis, S. cecembensis and S. kalamii resulted in values below 70 %. Strain MA9T could be differentiated genotypically and phenotypically from the recognized species of the genus Solibacillus. The isolate therefore represents a novel species, for which the name Solibacillus palustris sp. nov. is proposed, with the type strain MA9T (=KACC 22212T = LMG 32188T)
Three Fe(III)-reducing and nitrogen-fixing bacteria, Anaeromyxobacter terrae sp. nov., Anaeromyxobacter oryzisoli sp. nov. and Anaeromyxobacter soli sp. nov., isolated from paddy soil
Authors: Tang Rong , Yang Shang , Narsing Rao Manik Prabhu , Xie Cheng-Jie , Han Shuang , Yang Qiu-E , Rensing Christopher , Liu Guo-Hong , Yuan Yong , Zhou Shun-Gui
Published: February 2024

Three microaerophilic bacterial strains, designated SG22T, SG63T and SG29T were isolated from paddy soils in PR China. Cells of these strains were Gram-staining-negative and long rod-shaped. SG22T, SG63T and SG29T showed the highest 16S rRNA gene sequence similarities with the members of the genus Anaeromyxobacter. The results of phylogenetic and phylogenomic analysis also indicated that these strains clustered with members of the genus Anaeromyxobacter. The main respiratory menaquinone of SG22T, SG63T and SG29T was MK-8 and the major fatty acids were iso-C15 : 0, iso-C17 : 0 and C16 : 0. SG22T, SG29T and SG63T not only possessed iron reduction ability but also harboured genes (nifHDK) encoding nitrogenase. The genomic DNA G+C contents of SG22T, SG63T and SG29T ranged from 73.3 to 73.5 %. The average nucleotide identity (ANI) and digital DNA–DNA hybridisation (dDDH) values between SG22T, SG63T and SG29T and the closely related species of the genus Anaeromyxobacter were lower than the cut-off values (dDDH 70 % and ANI 95–96 %) for prokaryotic species delineation. On the basis of these results, strains SG22T, SG63T and SG29T represent three novel species within the genus Anaeromyxobacter, for which the names Anaeromyxobacter terrae sp. nov., Anaeromyxobacter oryzisoli sp. nov. and Anaeromyxobacter soli sp. nov., are proposed. The type strains are SG22T (= GDMCC 1.3185T = JCM 35581T), SG63T (= GDMCC 1.2914T = JCM 35124T) and SG29T (= GDMCC 1.2911T = JCM 35123T).
Beyond blast: enabling microbiologists to better extract literature, taxonomic distributions and gene neighbourhood information for protein families
Authors: Reed Colbie J. , Denise Rémi , Hourihan Jacob , Babor Jill , Jaroch Marshall , Martinelli Maria , Hutinet Geoffrey , de Crécy-Lagard Valérie
Published: February 2024

Capturing the published corpus of information on all members of a given protein family should be an essential step in any study focusing on specific members of that family. Using a previously gathered dataset of more than 280 references mentioning a member of the DUF34 (NIF3/Ngg1-interacting Factor 3) family, we evaluated the efficiency of different databases and search tools, and devised a workflow that experimentalists can use to capture the most information published on members of a protein family in the least amount of time. To complement this workflow, web-based platforms allowing for the exploration of protein family members across sequenced genomes or for the analysis of gene neighbourhood information were reviewed for their versatility and ease of use. Recommendations that can be used for experimentalist users, as well as educators, are provided and integrated within a customized, publicly accessible Wiki.
Immunotherapy Efficacy Prediction in Cancer: An Artificial Intelligence Approach with Unannotated H&E Whole-Slide Images
Authors: Conde Gabriel Domínguez , Qaiser Talha , Wu Evan , Andrea Carlos Eduardo de , Shields Jennifer , Artzi Ronen , RaviPrakash Harish , Irabor Kenneth , Metcalfe Paul , Reischl Joachim
Published: February 2024

Developing a solution to predict clinical outcomes for immunotherapy that is accurate, scalable, affordable, clinically meaningful, and globally accessible is an unmet medical need. Precise prediction of patient response to immunotherapy from pretreatment biopsy images will enable the delivery of immuno-oncology drugs to suitable patients and reduce the risk of administering unnecessary toxicity to patients who do not benefit from it. We propose an AI-based framework to produce stratifying algorithms that only need routinely obtained unannotated hematoxylin and eosin (H&E)-stained whole slide images. This design choice eliminates the need for pathologist annotations, ensuring affordability and scalability. Our solution, developed with data from 418 durvalumab patients, was validated both for head and neck squamous cell carcinoma and non-small cell lung cancer with data from 283 durvalumab patients, demonstrating its versatility and ease of adaptation for different indications. The results obtained using test data from clinical trials, different from training data, exhibit clinically meaningful improvement between those classified as positive and negative. For median overall survival (OS), the enhancement is in the range [55.9%, 198%] and [0.49, 0.70] for the hazard ratio for OS. For median progression-free survival (PFS), the improvement ranges within [39%, 195%], while the hazard ratio is within [0.46, 0.86] for PFS. Our solution complements the current biomarker, programmed death lig– and 1, for immunotherapy therapy, presenting an opportunity to develop more accurate solutions. In addition, as the algorithm was developed in a hypothesis-free approach, the analysis of the converged solution may enhance expert understanding of the pathomechanisms driving the response to immunotherapy. Its scalability and accuracy, combined with the AI-based engineering nature of the solution, bring the opportunity of being globally deployed using the cloud. Our technique has the potential to unlock opportunities not available for patients before by enabling the generation of efficient and affordable diagnoses for immunotherapy.
UniFed: A unified deep learning framework for segmentation of partially labelled, distributed neuroimaging data
Authors: Dinsdale Nicola K , Jenkinson Mark , Namburete Ana IL
Published: February 2024

It is essential to be able to combine datasets across imaging centres to represent the breadth of biological variability present in clinical populations. This, however, leads to two challenges: an increase in non-biological variance due to scanner differences, known as theharmonisationproblem, and, data privacy concerns due to the inherently personal nature of medical images. Federated learning has been proposed to train deep learning models on distributed data; however, the majority of approaches assume fully labelled data at each participating site, which is unlikely to exist due to the time and skill required to produce manual segmentation labels. Further, they assume all of the sites are available for training. Thus, we introduceUniFed, a unified federated harmonisation framework that enables three key processes to be completed: 1) the training of a federated harmonisation network, 2) the selection of the most appropriate pretrained model for a new unseen site, and 3) the incorporation of a new site into the harmonised federation. We show that when working with partially labelled distributed datasets,UniFedproduces high-quality segmentations and enable all sites to benefit from the knowledge of the federation. The code is available athttps://github.com/nkdinsdale/UniFed.
Self-regulation of the DNA N6-adenine methyltransferase AMT1 in the unicellular eukaryoteTetrahymena thermophila
Authors: Duan Lili , Li Haicheng , Ju Aili , Zhang Zhe , Niu Junhua , Zhang Yumiao , Diao Jinghan , Kataoka Kensuke , Ma Honggang , Song Ni , Gao Shan , Wang Yuanyuan
Published: February 2024

DNA N6-adenine methylation (6mA) is involved in gene transcription as a potential epigenetic mark in eukaryotes. Despite the reported methyltransferase (MTase) for 6mA methylation in several eukaryotes, the regulatory mechanisms that govern the activity of 6mA MTase remain elusive. Here, we exploited the 6mA MTase AMT1 to elucidate its self-regulation in the unicellular eukaryoteTetrahymena thermophila. Firstly, detailed endogenous localization of AMT1 was delineated both in vegetative and sexual stages, revealing a correlation between the 6mA reestablishment in the new MAC and the occurrence of zygotically expressed AMT1. Catalytically inactive AMT1 reduced 6mA level on theAMT1gene and its expression level, suggesting that AMT1 modulated its own transcription via 6mA. Furthermore, AMT1-dependent 6mA regulated the transcription of its target genes thus affecting the cell fitness, as demonstrated by manipulating the dosage of AMT1 using AMT1-RNAi strains. Our findings unveil a positive feedback loop of transcriptional activation on theAMT1gene and highlight the crucial role of AMT1-dependent 6mA for gene transcription.
High-fat and high-carbohydrate diets worsen the mouse brain susceptibility to damage produced by enterohemorrhagicEscherichia coliShiga toxin 2
Authors: Arenas-Mosquera D , Cerny N , Cangelosi A , Geoghegan PA , Malchiodi EL , De Marzi M , Pinto A , Goldstein J
Published: February 2024

Background

Nutrition quality could be one of the reasons why, in the face of a Shiga toxin-producing enterohaemorrhagicEscherichia colioutbreak, some patients experience more profound deleterious effects than others, including unfortunate deaths. Thus, the aim of this study was to determine whether high-fat and/or high-carbohydrate diets could negatively modulate the deleterious action of Shiga toxin 2 on ventral anterior and ventral lateral thalamic nuclei and the internal capsule, the neurological centers responsible for motor activity.

Methods

Mice were fed a regular, high-fat, high-carbohydrate diet or a combination of both previous to the intravenous administration of Shiga toxin 2 or vehicle. Four days after intravenous administration, mice were subjected to behavioral tests and then sacrificed for histological and immunofluorescence assays to determine alterations in the neurovascular unit at the cellular and functional levels. Statistical analysis was performed using one-way analysis of variance followed by Bonferronipost hoctest. The criterion for significance was p = 0.0001 for all experiments.

Results

The high-fat and the high-carbohydrate diets significantly heightened the deleterious effect of Stx2, while the combination of both diets yielded the worst results, including endothelial glycocalyx and oligodendrocyte alterations, astrocyte and microglial reactivity, neurodegeneration, and motor and sensitivity impairment.

Conclusions

In view of the results presented here, poor nutrition could negatively influence patients affected by Stx2 at a neurological level. Systemic effects, however, cannot be ruled out.
Active Matter under Control: Insights from Response Theory
Authors: Davis Luke K. , Proesmans Karel , Fodor Étienne
Published: February 2024

Active constituents burn fuel to sustain individual motion, giving rise to collective effects that are not seen in systems at thermal equilibrium, such as phase separation with purely repulsive interactions. There is a great potential in harnessing the striking phenomenology of active matter to build novel controllable and responsive materials that surpass passive ones. Yet, we currently lack a systematic roadmap to predict the protocols driving active systems between different states in a way that is thermodynamically optimal. Equilibrium thermodynamics is an inadequate foundation to this end, due to the dissipation rate arising from the constant fuel consumption in active matter. Here, we derive and implement a versatile framework for the thermodynamic control of active matter. Combining recent developments in stochastic thermodynamics and response theory, our approach shows how to find the optimal control for either continuous- or discrete-state active systems operating out of equilibrium. Our results open the door to designing novel active materials that are not only built to stabilize specific nonequilibrium collective states but are also optimized to switch between different states at minimum dissipation.

Published by the American Physical Society
2024
Air pollution and stock market returns: actual effect vs public attention in an Indian context
Authors: Singh Anirudh , Chakraborty Madhumita
Published: February 2024

Purpose

This paper analyzes how air pollution and the public attention to it influence the returns of stocks in the Indian context.

Design/methodology/approach

The study uses firm-level data for the stocks listed on National Stock Exchange in India. Air quality is measured using the Air Quality Index (AQI) values provided by US Embassy and Consulates’ Air Quality Monitor in India. Google Search Volume Index (GSVI) of the relevant terms acts as the measure of public attention. Appropriate regression models are used to address how AQI and attention influence stock returns.

Findings

It is observed that degrading air quality alone is unable to explain the stock returns. It is the combined effect of increasing AQI and subsequent rise in associated public attention that negatively impacts these returns. Returns of firms with poor environment score component in their environmental, social, governance (ESG) scores are more negatively affected compared to firms with higher environment scores.

Practical implications

Investors can make use of this knowledge to formulate effective trading strategies and ensure higher chances of profitability in the share market.

Originality/value

To the knowledge of the authors, no earlier study has investigated the effects of AQI and attention together to explain stock price movements. The study is conducted in the Indian context providing a unique opportunity to study the behavioral impact of these effects in one of the fastest growing global economies, which is also plagued by an alarming increase in ambient air pollution.
Individual variation in home‐range across an ocean basin and links to habitat quality and management
Authors: Hays Graeme C. , Rattray Alex , Shimada Takahiro , Esteban Nicole
Published: February 2024

Overgrazing may lead to management intervention (e.g. culling, animal relocation) to try and prevent habitat destruction. Overgrazing leading to seagrass meadow collapse has been recorded for green turtles (Chelonia mydas) at several sites around the world, although the generality of this phenomenon and the need for intervention to prevent widespread seagrass destruction is unknown.

Where turtles have degraded seagrass meadows, home‐ranges are expected to be large and turtles will relocate as meadows are destroyed. We used high resolution Fastloc GPS tracking (n = 32 individuals, mean = 171 days per individual, SD = 99) to record the home‐range of adult green turtles at foraging sites spanning 4523 km of longitude across the Western Indian Ocean. Contrary to predictions if overgrazing was occurring, we recorded small home‐ranges and turtles rarely relocated their daytime foraging areas.

Based on all locations received, the mean 50% and 95% utilisation distributions (UD50 and UD95) were 2.4 km2 (SD = 2.7) and 15.4 km2 (SD = 17.7). Space use was often particularly small at night, when turtles rest, averaging 11% of the overall space use with the mean night‐time UD50 and UD95 being 0.15 km2 (SD = 0.1) and 1.1 km2 (SD = 0.8), respectively. Variation in home‐range across individuals was not influenced by the data volume (number of locations per day, duration of tracking) or animal size (carapace length) but increased significantly as the distance between the centre of day and night areas increased, that is individuals that had a larger daily commute had the larger home‐ranges.

Synthesis and applications. Comparisons with home‐range estimates from 16 previous studies, showed that those we recorded are among the smallest for adult green turtles globally. These results suggest that despite population size increases at several major nesting sites in the Western Indian Ocean, green turtles are generally not destroying the seagrass meadows on which they forage and so management intervention to prevent overgrazing is not needed. In this way, our work illustrates how movement data may inform management decisions for green turtles. Further targeted work on the seagrass ecosystem health could help confirm this suggestion.
Endogenous rhythmic growth and ectomycorrhizal fungi modulate priming of antiherbivore defences in subsequently formed new leaves of oak trees
Authors: Fernández I. , Bouffaud M. L. , Martínez‐Medina A. , Schädler M. , Tarkka M. T. , Weinhold A. , van Dam N. M. , Herrmann S. , Buscot F.
Published: February 2024

Priming of plant defences provides increased plant protection against herbivores and reduces the allocation costs of defence. Defence priming in woody plants remains obscure, in particular, due to plant development traits such as endogenous rhythmic growth.

By using bioassays with oak microcuttings (Quercus robur) and combining transcriptomic and metabolomic analyses, we investigated how leaf herbivory by Lymantria dispar and root inoculation with the ectomycorrhizal fungus Piloderma croceum prime oak defences. We further investigated how defence priming is modulated by the rhythmic growth of the oaks.

A first herbivory challenge in oak leaves primed newly grown leaves for enhanced induction of jasmonic acid (JA)‐related direct defences, or enhanced emission of volatiles, depending on the specific growth stage at which the plants were first challenged. Root inoculation with Piloderma abolished the enhanced induction of JA‐related defences and volatile emission.

Synthesis: Our results indicate that a first herbivore attack primes direct and indirect defences of newly formed oak leaves and that the specific display of defence priming is regulated by rhythmic growth, and modulated by the interaction Piloderma. Our results show that the priming memory in oaks can be transmitted to the next growth cycle, to the leaves of the new shoot unit.
m‐Aminophenylacetylene induces maternal care in a predatory spider
Authors: Chen Yunru , Yu Na , Dong Shuchen , Li Guanqun , Pan Huiya , Guo Zonglei , Liu Zewen
Published: February 2024

Maternal care is critically important for the survival of offspring in various animals. Spiders in the family Lycosidae are known for their hunting ability and maternal care behaviors. Predation on newly hatched spiderlings (pulli) by mother spiders decreases when they come into contact, and they carry the pulli on their dorsal surface. However, the factors inducing maternal care in lycosid spiders have not been elucidated. In this study, we investigated maternal care in Pardosa pseudoannulata (Araneae, Lycosidae) females. We proposed that the physical interaction between pulli and mother spiders induces maternal care via m‐aminophenylacetylene (m‐A), a novel regulator of maternal care. The presence of pulli on the dorsal abdomen of non‐mother spiders suppressed pulli predation and increased the pulli‐carrying rate, and the absence of pulli on the mother spiders increased pulli predation and decreased the pulli‐carrying rate. The compound m‐A was abundant in mother spiders, and it could be induced in non‐mother spiders when they carried pulli. The topical application of m‐A to non‐mother spiders and m‐A injection decreased pulli predation and increased the pulli‐carrying rate, respectively; these findings indicate that m‐A in both internal tissues and the integument is required for the induction of maternal care behavior, and the interaction between pulli and females induces the production of m‐A. In‐depth study of the regulatory mechanism of maternal care will enhance our understanding of spider biology and behavior.