bluuebunny/crossref_metadata_2025 huggingface dataset:
Integrierte Tierärztliche Bestandsbetreuung und Selektives
Trockenstellen in Deutschland
Authors: Sonnewald-Daum Tanja , Obster Fabian , Mansfeld Rolf
Published: November 2023

Ziel Ermittlung von aktuellen Informationen über Entwicklung und
Durchführung der Integrierten Tierärztlichen Bestandsbetreuung
(ITB) sowie Verbreitung des Selektiven Trockenstellens (ST) in deutschen
Tierarztpraxen und Milchviehbetrieben. Zudem Darstellung von Unterschieden oder
Gemeinsamkeiten zwischen Tierärzten mit und ohne ITB in Bezug auf die
Anwendung von Verfahren zum ST.

Material und Methoden 600 Fragebögen wurden im Rahmen von 7
Fortbildungen an Nutztierpraktiker verteilt. Die Teilnahme war freiwillig und
anonym. Die Datenauswertung erfolgte mittels deskriptiver Statistik, linearer
und logistischer Regression.

Ergebnisse Der Rücklauf betrug 39,3% (n=236). Eine
ITB wurde von 54,2% (n=128) der Tierärzte
durchgeführt. Von 75% (n=177) der Tierärzte
wurden Verfahren zum ST angewendet. Dabei wurden verschiedene
Entscheidungskriterien auf Herden- (81,6%, n=142) und
Einzeltierebene (97,7%, n=172) genutzt. Eine Erfolgskontrolle
des Verfahrens wurde häufiger in Betrieben von Tierärzten mit
ITB (66%, n=66) als ohne ITB (41%, n=28)
durchgeführt. Je mehr Betriebe im Rahmen einer ITB betreut wurden, desto
höher war der Anteil der Betriebe, in denen selektiv trockengestellt
wurde. Eine steigende Chance auf eine gleichbleibende oder verbesserte
Eutergesundheit war mit ST-Betrieben assoziiert, in denen gleichzeitig eine ITB
durchgeführt wurde (OR: 1,025; p<0,05). Die Beratung bei
Problemen in der Trockenstehzeit (OR: 3,639; p<0,05), die
Häufigkeit, mit der Tierärzte die Landwirte (OR: 1,595;
p<0,05) und Landwirte die Tierärzte auf ST ansprachen (OR:
1,538; p<0,05), sowie die Beratungshäufigkeit zum
Trockenstellmanagement (OR:1,608; p<0,05) hatten einen positiven
Einfluss auf die Wahrscheinlichkeit, ob ST in einem Betrieb durchgeführt
wurde und ob dies erfolgreich war.

Schlussfolgerungen Sowohl ITB als auch ST sind nach vorliegenden Daten
etablierte Bestandteile der tierärztlichen Tätigkeit in
Rinderpraxen. Das ST wird in der Praxis zum Teil im Rahmen kontrollierter
Verfahren mit Erfolgskontrolle umgesetzt. Die Durchführung einer ITB war
positiv mit der Anzahl der Betriebe assoziiert, in denen selektiv
trockengestellt wurde, und mit dem Eutergesundheitsstatus, wenn in einem Betrieb
ITB und ST kombiniert durchgeführt wurden. Beratungsangebot und
-häufigkeit der Tierärzte haben einen wesentlichen Einfluss auf
eine Antibiotikareduktion durch ST.
Total removal of the fourth metacarpal bone in an Icelandic
horse
Authors: Vidović Aleksandar , Kuhn Sabrina
Published: November 2023

Fractures of the splint bones are the most common fractures in horses. Various
treatment options for splint bone fractures (MC/MT II and IV), including
conservative and surgical management, have been described. This report describes
an acute splint bone fracture due to external trauma in a 17-year-old Icelandic
mare. The fracture was diagnosed as an open multifragment fracture of the
proximal third of the fourth metacarpal bone (MCIV) in the right front limb.
Surgery was performed with the horse under general anaesthesia. The distal
fragments were removed, and the distal part of the proximal remnant splint bone
was cut with an osteotome. During the postoperative period, a routine
x-ray-control two days after surgery showed a dislocated fracture of the
remaining proximal part of the fourth metacarpal bone. In a second surgery, the
proximal part of MCIV was entirely removed. After a reconvalescence period of 5
month, the horse reached her previous level of performance as a leisure horse.
The mare is still free of lameness 6 years after the incident.
Reactions of 5-(Trialkyl)silylpent-1-en-4-yn-3-ones with Hydrazines: Original Synthetic Routes to Luminescent Substances Containing Azole Motifs
Authors: Golovanov Alexander A. , Odin Ivan S. , Gordon Kareem V. , Itakhunov Radik N. , Gusev Dmitry M. , Sokov Sergey A. , Vologzhanina Anna V. , Grabovskiy Stanislav A. , Sosnin Ilya M. , Ukolov Anton I. , Orlova Olga I. , Lazarenko Vladimir A. , Dorovatovskii Pavel V. , Darmoroz Darina D. , Piven Anastasiia O. , Orlova Tetiana
Published: November 2023

On the basis of the selective reactions of hydrazines with trialkylsilyl-substituted cross-conjugated enynones (pent-1-en-4-yn-3-ones) as fundamental building blocks, this work presents the developed common methodology for the synthesis of polysubstituted luminescent derivatives of acetylenic pyrazolines, pyrazoles, and combined polyheterocycles containing structural fragments from pyrazolines, isoxazoles, thiophenes, thiazoles, benzo[d]thiazoles, and benzo[d]imidazoles. In reactions with hydrazine and its monosubstituted aromatic and heteroaromatic derivatives, the mentioned pent-1-en-4-yn-3-ones, containing Me3Si, Et3Si, and t-BuMe2Si groups at the triple bond, give 3-(trialkylsilyl)ethynylpyrazolines. Following stages of desilylation and 1,3-dipolar cycloaddition with nitrile oxides, the 3-(trialkylsilyl)ethynylpyrazolines provide the formation of combined polyheterocyclic derivatives. Thus, a one-pot synthetic route to pyrazoline-containing isoxazoles from cross-conjugated enynones, arylhydrazines, and α-chlorobenzaldoximes has been developed. Some aspects of cyclocondensation mechanism and luminescent properties of synthesized azoles derivatives were examined.
Conversion from memory to threshold resistance switching behavior by modulating compliance current
Authors: Xu Jing , Dong Zhihu , Liu Yong , Zhu Yuanyuan , Wang Hongjun , Cheng Jinbing , Zheng Changbo , Xiong Rui
Published: November 2023

The volatile and nonvolatile resistance switching (RS) characteristics can be, respectively, used for the selector and memristor, which have received much attention. Thus, it is essential to find a simple and effective method to control the specific RS behavior of NbOx materials due to the co-occurrence of memory RS and threshold RS behaviors. Here, the NbOx film with a thickness of 100 nm was prepared by magnetron sputtering at 80 °C. The tungsten steel tip/NbOx/Pt device exhibited the co-existence of memory RS and threshold RS behaviors. By properly regulating compliance current (Icc), the specified memory and threshold RS behaviors were observed: the memory RS behavior occurred with an Icc of 5 mA, the threshold RS behavior occurred with an Icc of 10 mA, and integrated one selector-one-RRAM (resistive random access memory) (1S1R) RS behavior occurred with an Icc of 50 mA. Moreover, individual RS behavior showed good performance, e.g., good stability of memory RS, good repeatability and concentrated voltage distribution of threshold RS. The memory RS behavior occurred mainly due to the formation and fracture of oxygen vacancy conductive filaments (CFs). Meanwhile, mediated by local Joule heating, thermally induced conductivity change was responsible for the threshold RS behavior. Under an Icc of 50 mA, the oxygen vacancy CFs and a thermally induced conductivity change triggered the 1S1R RS behavior, which significantly suppressed the leakage current in RRAM 3D integrated structures. This work provides an efficient and convenient method for modulating and obtaining the desired RS behavior and better understanding the conversion mechanism between them.
Polarization-insensitive silicon optic switch based on mode manipulated power splitters and phase shifters
Authors: Zhao Shi , Chen Jingye , Dai Daoxin , Shi Yaocheng
Published: November 2023

A polarization-insensitive thermo-optic switch is proposed and demonstrated on the silicon-on-insulator platform with a 220 nm silicon core layer. The present device is based on the Mach–Zehnder interferometer structure, consisting of polarization-insensitive power splitters and polarization-insensitive phase shifters (PIPSs). The polarization-insensitive power splitter has been realized by employing an adiabatic directional coupler, which utilizes the fast adiabatic mode evolution by introducing cubic Bézier curves on outer contours, providing broadband 3-dB power splitting for TE and TM polarization modes with only 70 µm coupling length. For the novel PIPSs, the ridge waveguide with large aspect ratio, based on the mode hybridness property, could obtain the same power consumption (Pπ) for an optical switch working at TE and TM polarizations. Experimental results indicate that the measured insertion losses are less than 2 dB and the extinction ratios are larger than 15 dB over a 40 nm wavelength band (covering the C-band).
Thermal conductivity and fractal texture formation in β-Si3N4/polyvinylidene fluoride composites
Authors: Munakata Fumio , Ogiya Taito , Konemura Ryo , Sato Yoshihiro , Kitani Suguru , Kawaji Hitoshi
Published: November 2023

Additive incorporation into polymers can enhance properties, such as the dielectric constant and thermal conductivity. The improved properties of polymer composites have largely been attributed to aggregate and network formation, but the influence of material texture requires clarification. Herein, the relationship between the texture of composite materials and thermal conductivity was investigated based on the fractal nature of composites consisting of polyvinylidene fluoride (PVDF) with β-Si3N4 (SN) as a high-thermal-conductivity filler. The SN particle groups were found to contribute to the formation of thermal conduction paths in the composite material and, thus, improve the thermal conductivity. The characteristics of the particle group clusters involved in SN particle percolation were elucidated by analyzing the interactions between multiple particles as a function of the amount of each fractal dimension. In addition, based on the statistical relationships obtained from the multifractal analysis, the strengths of the interactions between particles during thermal conduction path formation were estimated. Overall, the texture of the SN/PVDF material was characterized by local particle group formation (self-assembly) and subsequent global particle group network construction (self-organization), depending on the amount of SN added. These results suggest that multifractal dimensions can be used as material design indices for the texture of polymer composites.
A nonvolatile memory element for integration with superconducting electronics
Authors: Pot C. , Holmes-Hewett W. F. , Anton E.-M. , Miller J. D. , Ruck B. J. , Trodahl H. J.
Published: November 2023

We demonstrate a nonvolatile cryogenic magnetic memory element needed to support emerging superconducting- and quantum-computing technologies. The central element is a switchable tri-layer thin film magnetic dot comprising two semiconducting ferromagnetic GdxSm1−xN layers separated by an exchange-blocking Al layer. The materials are explored for their tunable magnetic responses, the potential to engineer compensating magnetic moments in the anti-parallel tri-layers. The stability of the parallel and anti-parallel states and the reproducibility over repeated cycles are also demonstrated. We show that the tri-layer stacks can be formed into dots as small as 4 μm diameter, without affecting their magnetic behavior.
Particle binding capacity of snail saliva
Authors: Krings Wencke , Gorb Stanislav N.
Published: November 2023

Gastropods forage with their radula, a thin chitinous membrane with embedded teeth, which scratch across the substrate to lose food particles. During this interaction, the risk of loosening particles is obvious without having a specialized mechanism holding them on the tooth surface. As mucus secretions are essential in molluscan life cycles and the locomotion and attachment gels are known to have an instant high adhesion, we have hypothesized that the saliva could support particle retention during feeding. As adhesion of snail saliva was not studied before, we present here an experimental setup to test its particle-binding capacity using a large land snail (Lissachatina fulica, Stylommatophora, Heterobranchia). This experiment was also applied to the gels produced by the snail foot for comparison and can be potentially applied to various fluids present at a small volume in the future. We found, that the saliva has high particle retention capacity that is comparable to the foot glue of the snail. To gain some insight into the properties of the saliva, we additionally studied it in the scanning electron microscope, estimated its viscosity in a de-wetting experiment, and investigated its elemental composition using energy dispersive X-ray spectroscopy reveling higher contents of Ca, Zn and other potential cross-linkers similar to those found in the glue.
In pursuit of degenerative brain disease diagnosis: Dementia biomarkers detected by DNA aptamer-attached portable graphene biosensor
Authors: Bodily Tyler Andrew , Ramanathan Anirudh , Wei Shanhong , Karkisaval Abhijith , Bhatt Nemil , Jerez Cynthia , Haque Md Anzarul , Ramil Armando , Heda Prachi , Wang Yi , Kumar Sanjeev , Leite Mikayla , Li Tie , Zhao Jianlong , Lal Ratnesh
Published: November 2023

Dementia is a brain disease which results in irreversible and progressive loss of cognition and motor activity. Despite global efforts, there is no simple and reliable diagnosis or treatment option. Current diagnosis involves indirect testing of commonly inaccessible biofluids and low-resolution brain imaging. We have developed a portable, wireless readout-based Graphene field-effect transistor (GFET) biosensor platform that can detect viruses, proteins, and small molecules with single-molecule sensitivity and specificity. We report the detection of three important amyloids, namely, Amyloid beta (Aβ), Tau (τ), and α-Synuclein (αS) using DNA aptamer nanoprobes. These amyloids were isolated, purified, and characterized from the autopsied brain tissues of Alzheimer’s Disease (AD) and Parkinson’s Disease (PD) patients. The limit of detection (LoD) of the sensor is 10 fM, 1–10 pM, 10–100 fM for Aβ, τ, and αS, respectively. Synthetic as well as autopsied brain-derived amyloids showed a statistically significant sensor response with respect to derived thresholds, confirming the ability to define diseased vs. nondiseased states. The detection of each amyloid was specific to their aptamers; Aβ, τ, and αS peptides when tested, respectively, with aptamers nonspecific to them showed statistically insignificant cross-reactivity. Thus, the aptamer-based GFET biosensor has high sensitivity and precision across a range of epidemiologically significant AD and PD variants. This portable diagnostic system would allow at-home and POC testing for neurodegenerative diseases globally.
Heterogenous biofilm mass-transport model replicates periphery sequestration of antibiotics in
Pseudomonas aeruginosa
PAO1 microcolonies
Authors: Prince Joshua , Jones A-Andrew D.
Published: November 2023

A model for antibiotic accumulation in bacterial biofilm microcolonies utilizing heterogenous porosity and attachment site profiles replicated the periphery sequestration reported in prior experimental studies on
Pseudomonas aeruginosa PAO1
biofilm cell clusters. These
P. aeruginosa
cell clusters are in vitro models of the chronic
P. aeruginosa
infections in cystic fibrosis patients which display recalcitrance to antibiotic treatments, leading to exacerbated morbidity and mortality. This resistance has been partially attributed to periphery sequestration, where antibiotics fail to penetrate biofilm cell clusters. The physical phenomena driving this periphery sequestration have not been definitively established. This paper introduces mathematical models to account for two proposed physical phenomena driving periphery sequestration: biofilm matrix attachment and volume-exclusion due to variable biofilm porosity. An antibiotic accumulation model which incorporated these phenomena better fit observed periphery sequestration data compared to previous models.
Translating gender in video games
Authors: Martínez Pleguezuelos Antonio Jesús
Published: November 2023

This article investigates the role of localization in the representation of different gender and sexuality
profiles in video games. Using Sara Ahmed’s queer phenomenology as a methodological framework, it analyzes the ideological and
cultural limitations that restrict the rewriting of minority sexualities and genders when the original versions are transferred to
other languages. The article begins by considering the generative capacities of translation as an agent that can discursively
construct the subject, before focusing on the implications of localization for the shaping of identities from a phenomenological
perspective to describe what conditions may lead to the appearance of translated queer paradigms in video games. The theoretical
approach is applied to selected examples and conclusions for the practice of localization and its academic study are drawn.
High sensitivity refractive index sensor based on double peanut-shaped and etched multimode fiber structures
Authors: Wei Huijing , Wang Fang , Wang Xu , Liu Yufang
Published: November 2023

A fiber optic refractive index (RI) sensor based on an etched multimode fiber (MMF) with a double peanut-shaped structure is proposed and experimentally demonstrated. The sensor consists of two peanut-shaped and a section of etched MMF tapered fiber structure. The excitation of the fundamental mode to higher-order modes is facilitated by using the beam splitting/coupling effect of the double peanut-shaped and etched taper structures, and the higher-order modes can be excited into an evanescent field. In the sensing medium, the stronger the evanescent field, the stronger the energy shock between the fiber and the sensing environment. Experimental results showed that the sensitivity was 326.52 nm/RUI and 823.91 nm/RUI when the etched waist taper diameter was 51.92 μm and the glycerol solution index ranged from 1.3395 to 1.3945 and 1.3945 to 1.4200, respectively. Compared to the MMF sensor structure without etching, the RI sensitivity is improved by about 2 times. In addition, the temperature characteristics of the sensor were investigated over a range of 30 °C–100 °C, and the results showed a maximum temperature sensitivity of only 30.24 pm °m−1. The sensor structure has a low-temperature sensitivity and the temperature effect on the RI measurement results is negligible within the allowable error range. The sensor has the advantages of simple fabrication, wide measurement range, good stability, low cost, and compact structure, which has potential application value in the field of RI detection.
Development of an analytical method for the determination of pesticides in tropical fruits by LC-QTOF-MS/MS after QuEChERS extraction sample cleanup and DLLME preconcentration
Authors: Sel Sabriye , Er Elif Öztürk , Koyuncu İkbal
Published: November 2023

In this study, QuEChERS extraction was combined with dispersive liquid–liquid microextraction (DLLME) to extract pesticides from tropical fruits for determination by a highly accurate and sensitive liquid chromatography-quadrupole time-of-flight mass spectrometry (LC-QTOF-MS/MS) system. The QuEChERS method served as a matrix clean-up tool and the DLLME method preconcentrated the analytes for their determination at trace levels. All parameter variables of the DLLME method were optimized to improve the extraction output and lower the limits of detection and quantification (LOD and LOQ) for all the analytes. Under the optimum experimental conditions, the LOD and LOQ values were found in the range of 0.004–0.013 and 0.27–0.61 μg l−1, respectively. The detection limits achieved by direct LC-QTOF-MS/MS analysis were increased by about 10–260 folds using the optimized DLLME method. To assess the accuracy and applicability of the developed method, spike recovery experiments on tropical fruits were carried out. The matrix matching calibration method was used to enhance the quantification accuracy of the analytes in kiwi, pineapple, and mango matrices, with percent recoveries ranging between 89 and 117%.
A multicentre retrospective study of lumbar sympathectomy for plantar hyperhidrosis: satisfaction and postoperative complications
Authors: Housset Marie , Dessertenne Grégory , Marchand Etienne , Daligault Mickaël , Maillard Hervé
Published: November 2023

Background

Primary plantar hyperhidrosis has a severe impact on quality of life and conservative treatments are only effective in the short term. Thoracic sympathectomy has proven its effectiveness in the treatment of palmar hyperhidrosis, but lumbar sympathectomy for plantar hyperhidrosis remains poorly described.

Objectives

To report the satisfaction of patients with primary plantar hyperhidrosis treated with mechanical lumbar sympathectomy as well as their postoperative complications.

Methods

This was a multicentre retrospective observational study of 16 patients with primary plantar hyperhidrosis, treated with mechanical lumbar sympathectomy from December 2012 to October 2022. Patients’ characteristics were collected from medical records. Quality of life, postoperative satisfaction and complications were evaluated using a standardized questionnaire.

Results

Lumbar sympathectomy was performed on 16 patients, 14 were women and 2 were men with a total of 31 procedures. Fourteen (88%) patients were satisfied and would recommend the surgery to other patients. Compensatory hyperhidrosis occurred in 75% of patients, recurrence of hyperhidrosis in 31% and sexual dysfunction in 19%.

Conclusions

Lumbar sympathectomy provides satisfying results for plantar hyperhidrosis with acceptable postoperative complications, regardless of sex. Compensatory hyperhidrosis was the most frequent complication but had no impact on patient satisfaction. In the literature, data on the risk of sexual dysfunction are reassuring and in our study only one of two men experienced transient ejaculation disorder.
Rachel Cusk’s New Realism: Gender, Power, Voice, and Genre in the Outline Trilogy
Authors: Holland Mary K
Published: November 2023

Rachel Cusk creates a new narrative form in the Outline trilogy—distanced, displaced first-person point of view—to create a safe position from which to speak truths about marriage and motherhood that she has been criticized for expressing in her nonfiction work. Eschewing linear plot and dominating perspective in favor of overheard stories, the novels also represent a new form of social realism that illustrates how listening and collaborative storytelling can communicate social critique. By incorporating elements of her life and nonfiction in the trilogy, Cusk creates a nexus of autobiography, fiction, essay, and memoir in which the suffering of women and the cruelty of misogyny register as visible and undeniably real, changing the fabric of social reality by rewriting the forms that represent it.
Electrographic flow mapping of persistent atrial fibrillation: intra- and inter-procedure reproducibility in the absence of ‘ground truth’
Authors: Reddy Vivek Y , Kong Melissa H , Petru Jan , Maan Abhishek , Funasako Moritoshi , Minami Kentaro , Ruppersberg Peter , Dukkipati Srinivas , Neuzil Petr
Published: November 2023

Aims

Validating mapping systems that identify atrial fibrillation (AF) sources (focal/rotational activity) is confounded by the absence of ground truth. A key concern of prior mapping technologies is spatiotemporal instability, manifesting as poor map reproducibility. Electrographic flow (EGF) employs a novel algorithm that visualizes atrial electrical wavefront propagation to identify putative AF sources. We analysed both intra- (3 min) and inter- (>3 months) procedure EGF map reproducibility.

Methods and results

In 23 persistent AF patients, after pulmonary vein isolation (PVI), EGF maps were generated from 3 serial 1 min recordings using a 64-electrode basket mapping catheter (triplets) at right and left atrial locations. Source prevalence from map triplets was compared between recordings. Per protocol, 12 patients returned for 3-month remapping (1 non-inducible): index procedure post-PVI EGF maps were compared with initial EGF remapping at 3-month redo. Intra-procedure reproducibility: analysing 224 map triplets (111 right atrium, 113 left atrium) revealed a high degree of map consistency with minimal min-to-min shifts: 97 triplets (43%), exact match of leading sources on all 3 maps; 95 triplets (42%), leading source within 1 electrode space on 2 of 3 maps; and 32 triplets (14%), chaotic leading source pattern. Average deviation in source prevalence over 60 s was low (6.4%). Inter-procedure reproducibility: spatiotemporal stability of EGF mapping >3 months was seen in 16 of 18 (89%) sources mapped in 12 patients with (re)inducible AF.

Conclusion

Electrographic flow mapping generates reproducible intra- and inter-procedural maps, providing rationale for randomized clinical trials targeting these putative AF sources.
Large variance in inbreeding within the Iberian wolf population
Authors: Salado Isabel , Preick Michaela , Lupiáñez-Corpas Natividad , Fernández-Gil Alberto , Vilà Carles , Hofreiter Michael , Leonard Jennifer A
Published: November 2023

The gray wolf (Canis lupus) population on the Iberian Peninsula was the largest in western and central Europe during most of the 20th century, with its size apparently never under a few hundred individuals. After partial legal protection in the 1970s in Spain, the northwest Iberian population increased to about 300 to 350 packs and then stabilized. In contrast to many current European wolf populations, which have been connected through gene flow, the Iberian wolf population has been isolated for decades. Here, we measured changes in genomic diversity and inbreeding through the last decades in a geographic context. We find that the level of genomic diversity in Iberian wolves is low compared with other Eurasian wolf populations. Despite population expansion in the last 50 years, some modern wolves had very high inbreeding, especially in the recently recolonized and historical edge areas. These individuals contrast with others with low inbreeding within the same population. The high variance in inbreeding despite population expansion seems associated with small-scale fragmentation of the range that is revealed by the genetic similarity between modern and historical samples from close localities despite being separated by decades, remaining differentiated from other individuals that are just over 100 km away, a small distance for a species with great dispersal capacity inhabiting a continuous range. This illustrates that, despite its demographically stable condition, the population would probably benefit from favoring connectivity within the population as well as genetic exchange with other European wolf populations to avoid excessive fragmentation and local inbreeding depression.
Fines, nonpayment, and revenues: evidence from speeding tickets
Authors: Christian Traxler , Libor Dušek
Published: November 2023

We estimate the effect of the level of fines on payment compliance and revenues collected from speeding tickets. Exploiting discontinuous increases in fines at speed cutoffs and reform-induced variation in these discontinuities, we implement two complementary regression discontinuity designs. The results consistently document small payment responses: a 10% increase in the fine (i.e., the payment obligation) induces a 1.2 percentage point decline in timely payments. The implied revenue elasticity is about 0.9. Expressed in absolute terms, a one-dollar increase in the fine translates into a roughly 60-cent increase in payments collected within 15 days (JEL H27, H26, K42).
CRP-Tree: a phylogenetic association test for binary traits
Authors: Zhang Julie , Preising Gabriel A , Schumer Molly , Palacios Julia A
Published: November 2023

An important problem in evolutionary genomics is to investigate whether a certain trait measured on each sample is associated with the sample phylogenetic tree. The phylogenetic tree represents the shared evolutionary history of the samples and it is usually estimated from molecular sequence data at a locus or from other type of genetic data. We propose a model for trait evolution inspired by the Chinese Restaurant Process that includes a parameter that controls the degree of preferential attachment, that is, the tendency of nodes in the tree to subtend from nodes of the same type. This model with no preferential attachment is equivalent to a structured coalescent model with simultaneous migration and coalescence events and serves as a null model. We derive a test for phylogenetic binary trait association with linear computational complexity and empirically demonstrate that it is more powerful than some other methods. We apply our test to study the phylogenetic association of some traits in swordtail fish, breast cancer, yellow fever virus, and influenza A H1N1 virus. R-package implementation of our methods is available at https://github.com/jyzhang27/CRPTree.
Extensive suprasternal dehiscence reconstruction with NPWT and advancement flaps following cardiac surgery
Authors: Juhasz Boglarka , Tamas Robert
Published: November 2023

Treatment of suprasternal wound infection (SSWI) following cardiac surgery is not a clearly developed procedure. We report our female patient’s secondary SSWI treatment following bypass surgery. An obese female patient with unstable angina underwent an urgent, uneventful off-pump coronary artery bypass operation. An SSWI appeared within a week. After negative pressure wound therapy (NPWT), the sternum was rewired. In the previously irradiated territory of the left breast necrosis formed, a plastic surgeon reconstructed a defect. This procedure failed NPWT was restarted again, and a secondary reconstructive plastic surgery intervention was necessary. Despite extensive tissue mobilization, the central part of the reconstructive area necrotized, and we had to cover it with a split thickness skin mash graft. The irradiation therapy increases the incidence of suprasternal and/or sternal infection. It was possible to manage large soft tissue defects with bilateral and rotational advancement flaps.
Great lengths: a review of website preservation activities at three American Universities with digital humanities centers
Authors: VandeCreek Drew
Published: November 2023

Sustaining grant funded digital humanities websites has become a major challenge in the field. Three American universities with digital humanities centers kept eight of nine websites funded by the United States National Endowment for the Humanities (1996–2003) online to 2022. Center personnel made website preservation a part of everyday operations without additional funds devoted to the task. Web software developed rapidly in this period, however and center staff members’ efforts often did not succeed in providing necessary updates. Funded materials became increasingly obsolete. The extent of center personnel’s efforts, compared with their results, suggests that their approach itself will in many cases prove unsustainable. In one case, a university shifted responsibility for a popular website to its library. The library completely rebuilt it, only to find that the resource had again become obsolete less than 10 years later. Reconstruction should therefore be understood as an ongoing process, and its cost and complexity suggest that many online resources will not benefit from it. A new approach converting websites to a static state can facilitate sustainability at lower cost, but it also requires resources for implementation. Two American funding agencies have recently made grants available for website preservation and reconstruction. Similar organizations in other parts of the world have not followed suit and should consider doing so. In the absence of a comprehensive effort to identify and evaluate legacy websites for preservation, the competitive process of securing grant awards can begin to determine which legacy websites will survive.
Decoding dissociation of sequence-specific protein–DNA complexes with non-equilibrium simulations
Authors: van Heesch Thor , Bolhuis Peter G , Vreede Jocelyne
Published: November 2023

Sequence-specific protein–DNA interactions are crucial in processes such as DNA organization, gene regulation and DNA replication. Obtaining detailed insights into the recognition mechanisms of protein–DNA complexes through experiments is hampered by a lack of resolution in both space and time. Here, we present a molecular simulation approach to quantify the sequence specificity of protein–DNA complexes, that yields results fast, and is generally applicable to any protein–DNA complex. The approach is based on molecular dynamics simulations in combination with a sophisticated steering potential and results in an estimate of the free energy difference of dissociation. We provide predictions of the nucleotide specific binding affinity of the minor groove binding Histone-like Nucleoid Structuring (H-NS) protein, that are in agreement with experimental data. Furthermore, our approach offers mechanistic insight into the process of dissociation. Applying our approach to the major groove binding ETS domain in complex with three different nucleotide sequences identified the high affinity consensus sequence, quantitatively in agreement with experiments. Our protocol facilitates quantitative prediction of protein–DNA complex stability, while also providing high resolution insights into recognition mechanisms. As such, our simulation approach has the potential to yield detailed and quantitative insights into biological processes involving sequence-specific protein–DNA interactions.
Pot1 promotes telomere DNA replication via the Stn1-Ten1 complex in fission yeast
Authors: Carvalho Borges Pâmela C , Bouabboune Chaïnez , Escandell Jose Miguel , Matmati Samah , Coulon Stéphane , Ferreira Miguel Godinho
Published: November 2023

Telomeres are nucleoprotein complexes that protect the chromosome-ends from eliciting DNA repair while ensuring their complete duplication. Pot1 is a subunit of telomere capping complex that binds to the G-rich overhang and inhibits the activation of DNA damage checkpoints. In this study, we explore new functions of fission yeast Pot1 by using a pot1-1 temperature sensitive mutant. We show that pot1 inactivation impairs telomere DNA replication resulting in the accumulation of ssDNA leading to the complete loss of telomeric DNA. Recruitment of Stn1 to telomeres, an auxiliary factor of DNA lagging strand synthesis, is reduced in pot1-1 mutants and overexpression of Stn1 rescues loss of telomeres and cell viability at restrictive temperature. We propose that Pot1 plays a crucial function in telomere DNA replication by recruiting Stn1-Ten1 and Polα-primase complex to telomeres via Tpz1, thus promoting lagging-strand DNA synthesis at stalled replication forks.
The function of BCL11B in base excision repair contributes to its dual role as an oncogene and a haplo-insufficient tumor suppressor gene
Authors: Vickridge Elise , Faraco Camila C F , Lo Fanny , Rahimian Hedyeh , Liu Zi Yang , Tehrani Payman S , Djerir Billel , Ramdzan Zubaidah M , Leduy Lam , Maréchal Alexandre , Gingras Anne-Claude , Nepveu Alain
Published: November 2023

Genetic studies in mice and human cancers established BCL11B as a haploinsufficient tumor suppressor gene. Paradoxically, BCL11B is overexpressed in some human cancers where its knockdown is synthetic lethal. We identified the BCL11B protein in a proximity-dependent biotinylation screen performed with the DNA glycosylase NTHL1. In vitro DNA repair assays demonstrated that both BCL11B and a small recombinant BCL11B213-560 protein lacking transcription regulation potential can stimulate the enzymatic activities of two base excision repair (BER) enzymes: NTHL1 and Pol β. In cells, BCL11B is rapidly recruited to sites of DNA damage caused by laser microirradiation. BCL11B knockdown delays, whereas ectopic expression of BCL11B213-560 accelerates, the repair of oxidative DNA damage. Inactivation of one BCL11B allele in TK6 lymphoblastoid cells causes an increase in spontaneous and radiation-induced mutation rates. In turn, ectopic expression of BCL11B213-560 cooperates with the RAS oncogene in cell transformation by reducing DNA damage and cellular senescence. These findings indicate that BCL11B functions as a BER accessory factor, safeguarding normal cells from acquiring mutations. Paradoxically, it also enables the survival of cancer cells that would otherwise undergo senescence or apoptosis due to oxidative DNA damage resulting from the elevated production of reactive oxygen species.
Ensembl 2024
Authors: Harrison Peter W , Amode M Ridwan , Austine-Orimoloye Olanrewaju , Azov Andrey G , Barba Matthieu , Barnes If , Becker Arne , Bennett Ruth , Berry Andrew , Bhai Jyothish , Bhurji Simarpreet Kaur , Boddu Sanjay , Branco Lins Paulo R , Brooks Lucy , Ramaraju Shashank Budhanuru , Campbell Lahcen I , Martinez Manuel Carbajo , Charkhchi Mehrnaz , Chougule Kapeel , Cockburn Alexander , Davidson Claire , De Silva Nishadi H , Dodiya Kamalkumar , Donaldson Sarah , El Houdaigui Bilal , Naboulsi Tamara El , Fatima Reham , Giron Carlos Garcia , Genez Thiago , Grigoriadis Dionysios , Ghattaoraya Gurpreet S , Martinez Jose Gonzalez , Gurbich Tatiana A , Hardy Matthew , Hollis Zoe , Hourlier Thibaut , Hunt Toby , Kay Mike , Kaykala Vinay , Le Tuan , Lemos Diana , Lodha Disha , Marques-Coelho Diego , Maslen Gareth , Merino Gabriela Alejandra , Mirabueno Louisse Paola , Mushtaq Aleena , Hossain Syed Nakib , Ogeh Denye N , Sakthivel Manoj Pandian , Parker Anne , Perry Malcolm , Piližota Ivana , Poppleton Daniel , Prosovetskaia Irina , Raj Shriya , Pérez-Silva José G , Salam Ahamed Imran Abdul , Saraf Shradha , Saraiva-Agostinho Nuno , Sheppard Dan , Sinha Swati , Sipos Botond , Sitnik Vasily , Stark William , Steed Emily , Suner Marie-Marthe , Surapaneni Likhitha , Sutinen Kyösti , Tricomi Francesca Floriana , Urbina-Gómez David , Veidenberg Andres , Walsh Thomas A , Ware Doreen , Wass Elizabeth , Willhoft Natalie L , Allen Jamie , Alvarez-Jarreta Jorge , Chakiachvili Marc , Flint Bethany , Giorgetti Stefano , Haggerty Leanne , Ilsley Garth R , Keatley Jon , Loveland Jane E , Moore Benjamin , Mudge Jonathan M , Naamati Guy , Tate John , Trevanion Stephen J , Winterbottom Andrea , Frankish Adam , Hunt Sarah E , Cunningham Fiona , Dyer Sarah , Finn Robert D , Martin Fergal J , Yates Andrew D
Published: November 2023

Ensembl (https://www.ensembl.org) is a freely available genomic resource that has produced high-quality annotations, tools, and services for vertebrates and model organisms for more than two decades. In recent years, there has been a dramatic shift in the genomic landscape, with a large increase in the number and phylogenetic breadth of high-quality reference genomes, alongside major advances in the pan-genome representations of higher species. In order to support these efforts and accelerate downstream research, Ensembl continues to focus on scaling for the rapid annotation of new genome assemblies, developing new methods for comparative analysis, and expanding the depth and quality of our genome annotations. This year we have continued our expansion to support global biodiversity research, doubling the number of annotated genomes we support on our Rapid Release site to over 1700, driven by our close collaboration with biodiversity projects such as Darwin Tree of Life. We have also strengthened support for key agricultural species, including the first regulatory builds for farmed animals, and have updated key tools and resources that support the global scientific community, notably the Ensembl Variant Effect Predictor. Ensembl data, software, and tools are freely available.
RefMetaPlant: a reference metabolome database for plants across five major phyla
Authors: Shi Han , Wu Xueting , Zhu Yan , Jiang Tao , Wang Zhengwei , Li Xuetong , Liu Jianju , Zhang Yingxue , Chen Feng , Gao Jinshan , Xu Xiaoyan , Zhang Guoqing , Xiao Ning , Feng Xianzhong , Zhang Peng , Wu Yongrui , Li Aihong , Chen Ping , Li Xuan
Published: November 2023

Plants are unique with tremendous chemical diversity and metabolic complexity, which is highlighted by estimates that green plants collectively produce metabolites numbering in the millions. Plant metabolites play crucial roles in all aspects of plant biology, like growth, development, stress responses, etc. However, the lack of a reference metabolome for plants, and paucity of high-quality standard compound spectral libraries and related analytical tools, have hindered the discovery and functional study of phytochemicals in plants. Here, by leveraging an advanced LC–MS platform, we generated untargeted mass spectral data from >150 plant species collected across the five major phyla. Using a self-developed computation protocol, we constructed reference metabolome for 153 plant species. A ‘Reference Metabolome Database for Plants’ (RefMetaPlant) was built to encompass the reference metabolome, integrated standard compound mass spectral libraries for annotation, and related query and analytical tools like ‘LC–MS/MS Query’, ‘RefMetaBlast’ and ‘CompoundLibBlast’ for searches and profiling of plant metabolome and metabolite identification. Analogous to a reference genome in genomic research, RefMetaPlant provides a powerful platform to support plant genome-scale metabolite analysis to promote knowledge/data sharing and collaboration in the field of metabolomics. RefMetaPlant is freely available at https://www.biosino.org/RefMetaDB/.
A new paradigm for molecular dynamics databases: the COVID-19 database, the legacy of a titanic community effort
Authors: Beltrán Daniel , Hospital Adam , Gelpí Josep Lluís , Orozco Modesto
Published: November 2023

Molecular dynamics (MD) simulations are keeping computers busy around the world, generating a huge amount of data that is typically not open to the scientific community. Pioneering efforts to ensure the safety and reusability of MD data have been based on the use of simple databases providing a limited set of standard analyses on single-short trajectories. Despite their value, these databases do not offer a true solution for the current community of MD users, who want a flexible analysis pipeline and the possibility to address huge non-Markovian ensembles of large systems. Here we present a new paradigm for MD databases, resilient to large systems and long trajectories, and designed to be compatible with modern MD simulations. The data are offered to the community through a web-based graphical user interface (GUI), implemented with state-of-the-art technology, which incorporates system-specific analysis designed by the trajectory providers. A REST API and associated Jupyter Notebooks are integrated into the platform, allowing fully customized meta-analysis by final users. The new technology is illustrated using a collection of trajectories obtained by the community in the context of the effort to fight the COVID-19 pandemic. The server is accessible at https://bioexcel-cv19.bsc.es/#/. It is free and open to all users and there are no login requirements. It is also integrated into the simulations section of the BioExcel-MolSSI COVID-19 Molecular Structure and Therapeutics Hub: https://covid.molssi.org/simulations/ and is part of the MDDB effort (https://mddbr.eu).
Chemical-tag-based semi-annotated metabolomics facilitates gene identification and specialized metabolic pathway elucidation in wheat
Authors: Zhu Anting , Liu Mengmeng , Tian Zhitao , Liu Wei , Hu Xin , Ao Min , Jia Jingqi , Shi Taotao , Liu Hongbo , Li Dongqin , Mao Hailiang , Su Handong , Yan Wenhao , Li Qiang , Lan Caixia , Fernie Alisdair R , Chen Wei
Published: November 2023

The importance of metabolite modification and species-specific metabolic pathways has long been recognized. However, linking the chemical structure of metabolites to gene function in order to explore the genetic and biochemical basis of metabolism has not yet been reported in wheat (Triticum aestivum). Here, we profiled metabolic fragment enrichment in wheat leaves and consequently applied chemical-tag-based semi-annotated metabolomics in a genome-wide association study in accessions of wheat. The studies revealed that all 1,483 quantified metabolites have at least one known functional group whose modification is tailored in an enzyme-catalyzed manner and eventually allows efficient candidate gene mining. A Triticeae crop-specific flavonoid pathway and its underlying metabolic gene cluster were elucidated in further functional studies. Additionally, upon overexpressing the major effect gene of the cluster TraesCS2B01G460000 (TaOMT24), the pathway was reconstructed in rice (Oryza sativa), which lacks this pathway. The reported workflow represents an efficient and unbiased approach for gene mining using forward genetics in hexaploid wheat. The resultant candidate gene list contains vast molecular resources for decoding the genetic architecture of complex traits and identifying valuable breeding targets and will ultimately aid in achieving wheat crop improvement.
Occupational quantitative exposure to crystalline silica, solvents and pesticides and risk of clinical forms of systemic sclerosis
Authors: Galli Gaël , De Pous-Gerardin Camille , Hanguehard Remi , Berthy Florine , Le Moal Cyril , Lourde Come , Barnetche Thomas , Skopinski Sophie , Contin-Bordes Cecile , Delva Fleur , Carles Camille , Truchetet Marie-Elise
Published: November 2023

Objectives

To estimate the association between SSc clinical phenotypes and quantitative occupational exposure to crystalline silica, chlorinated solvents, trichloroethylene and pesticides using job-exposure matrices.

Methods

In the VISS-EXPOSITION transversal study, data on declarative occupational exposure to crystalline silica, solvents and pesticides were retrieved. In parallel, the lifetime occupational history was evaluated using a questionnaire and cursus laboris for SSc patients followed at Bordeaux University Hospital (France). Using job-exposure matrices, we assessed patients’ occupational exposure in relation to relevant clinical phenotypic forms of the disease.

Results

Toxic exposure to crystalline silica and pesticides is underestimated by patients. Non-biased job-exposure matrices retrieved more exposed patients than the declarative assessment (10.1% of patients by job-exposure matrices vs 6.3% by declaration for crystalline silica and 25.9% vs 12.2% for pesticides). Patients overestimate their solvent exposure (7.9% for chlorinated solvents and 4.8% for trichlorethylene assessed by job-exposure matrices and 24.4% declarative exposure to solvents at large). Clinical form evaluation revealed a non-significant trend toward an increased risk of crystalline silica occupational exposure in the pulmonary fibrotic group of SSc patients [odds ratio (OR) 3.12 (95% CI 0.80, 12.15)]. We also observed a non-significant trend toward an elevated OR ([2.89 (95% CI 0.93, 8.95)] for chlorinated solvent occupational exposure and the vascular phenotype of SSc. Of note, pesticide occupational exposure evaluation represents one of the largest to date in SSc patients.

Conclusion

This study emphasizes that many exposed SSc patients are unaware of their occupational exposure. Job-exposure matrices allow better exposure screening for SSc secondary prevention and occupational exposure compensation.

Clinical trial registration

clinicaltrials.gov (https://www.clinicaltrials.gov), NCT03543956