bluuebunny/crossref_metadata_2025 huggingface dataset:
Design of toothed belt driven screw vacuum pumps
Authors: Müller R , Dreifert T , Hellmig A
Published: December 2024

Most screw vacuum pumps use oil-lubricated gears for timing of the rotors. An alternative is a toothed belt to drive and synchronise the screw rotors. In combination with grease-lubricated bearings this drive concept allows the design of completely oil-free pumps. However, belts are less accurate in terms of timing, hence the design of efficient pumps is challenging. In this paper, the development of a new series of belt driven dry screw vacuum pumps is discussed. It covers the overall pump concept including cooling system, material selection and noise damping. Particular attention is paid to the design of the screw rotors with respect to the properties of the belt drive. It is shown that the disadvantage of the inaccurate timing and the need for wide rotor to rotor clearance can be overcome with a high number of wraps. Furthermore, it gives insight to applications and practical field experience.
Predicting the fracture forming limit of 5754-O aluminum alloy by finite element simulation
Authors: Yan Bin , Zhang Guocheng , Liu Xiaoli , Yin Xiaolin
Published: December 2024

Aluminum alloy has the advantages of low specific gravity, easy processing and good welding performance, so it is widely used on automobiles to achieve lightweighting. Forming limit diagram (FLD) is the most intuitive method for evaluating and analyzing the forming performance of aluminum alloys. Standard forming limit tests are complex and costly. To simplify test procedures of the formability for 5754-O aluminum alloys, three tests including uniaxial tensile, deep drawn cup and dome stretching tests were established through ABAQUS finite element software. The principal and secondary strain values at the time of fracture were extracted to construct the forming limit curve at fracture (FLCF). In order to verify the accuracy of the simulation results, corresponding experiments were conducted. The finite element simulation results match the experimental results, thereby verifying the accuracy of the finite element simulation. The method presented in this paper enables quick prediction of the formability of aluminum alloy.
Can political connection promote policy advocacy of social work organizations in China?
Authors: Xu Yang , Ren Fengjia , Wu Wenzhao , Enjian Wang
Published: December 2024

Policy advocacy is an important function and service content of social work organizations. The role of political connection in policy advocacy by social work organizations is controversial and has not been fully discussed in China. The study examined the association between political connection and policy advocacy and the moderating effects of executives’ specialization, among social work organizations in China. Based on a sample of 687 organizations and the Oprobit Regression Model method, the findings confirmed that political connection was positively related to social work organizations’ policy advocacy. Also, the positive effect between political connection and policy advocacy was moderated by executives’ specialization. Specifically, the positive effect between political connection and policy advocacy was more substantial when executives of social work organizations had a higher level of specialization. The results of this study enrich the empirical research on social work policy practice and provide a reference for the debate on political connection and policy advocacy.
Free Trade Agreements and the movement of business people
Authors: Mayer Thierry , Rapoport Hillel , Umana-Dajud Camilo
Published: December 2024

Using provisions to ease the movement of business visitors in trade agreements, we show that removing barriers to the movement of business people promotes trade. We document the increasing complexity of Free Trade Agreements (FTAs) and develop an algorithm that combines machine learning and text analysis techniques to examine the content of FTAs. We use the algorithm to determine which FTAs include provisions to facilitate the movement of business people and whether these are included in dispute settlement mechanisms. We show that provisions facilitating business travel are effective in promoting them and eventually increase bilateral trade flows. The paper provides (indirect) evidence of the role of face-to-face interaction on aggregate bilateral trade flows.
Pro's and con's of different blocks for postoperative analgesia after video-assisted thoracic surgery
Authors: Karakaya M. Ahmet , Yapici Davud , Bingül Emre Sertac , Turhan Özlem , Şentürk Mert
Published: December 2024

Purpose of review

Although there are a lot of studies examining the effects of different blocks for postoperative analgesia after video-assisted thoracic surgery (VATS), the results are controversial.

Recent findings

Paravertebral block, serratus anterior plane block and erector spinae plane block appear to be effective and beneficial for post-VATS analgesia, but probably in different manners.

All three blocks can be suggested for daily practice, the choice should be based on personal experience and preference of the anesthetist. Better studies are required for objective decision.
Enhancing Tracheostomy Care
Authors: Abu Ejheisheh Moath , Ayed Ahmad , Salameh Basma , Salameh Waed A. , Obeyat Alaa H. , Melhem Riham H. , Alkhatib Sanaa , Hammad Bahaaeddin M. , ALBashtawy Mohammed , Batran Ahmad
Published: December 2024

Patients requiring continuous mechanical ventilation benefit from easier airway management through tracheostomy, a standard treatment in critical care. However, gaps in nurses’ comprehension of tracheostomy car can lead to complications such as infections and airway blockages. Therefore, understanding nurses’ competency in tracheostomy care is essential for enhancing patient outcomes in intensive care units (ICUs). A cross-sectional study was conducted in the southern West Bank of Palestine among 237 nurses working in ICUs to assess their level of knowledge in tracheostomy care. Data were gathered via a structured questionnaire and analyzed using inferential tests and descriptive. Most nurses showed moderate knowledge of tracheostomy care, with significant differences observed based on age, gender, years of experience, and educational level. To significantly improve patient outcomes and safety in ICUs, it is imperative that nurses participate in continuous education and training programs focused on tracheostomy care.
Intramuscular Myxoma in the Thenar Eminence: Literature Review and a Rare Case Report
Authors: Jarrar Salma I. , Al Lahham Salim N.
Published: December 2024

Intramuscular myxoma (IM) is a rare benign soft-tissue neoplasm that most commonly involves the thigh muscles. It presents as a painless, solitary, slow-growing mass. The definitive diagnosis of IM can only be made by histopathological examination of the lesion. IM of the hand is extremely rare, with less than 5 cases being reported in the thenar eminence. Here we present a 54-year-old woman with a 10-year history of IM in the thenar eminence muscles.
Multicentric national Italian analysis of textbook outcome in colorectal cancer surgery: The ATOCCS Study protocol on behalf of the Italian Surgical Association (ACOI, Associazione Chirurghi Ospedalieri Italiani)
Authors: Marano Luigi , Mineccia Michela , Brillantino Antonio , Andreuccetti Jacopo , Farina Massimo , Lamacchia Giuseppe , Ranucci Chiara , Armellino Mariano Fortunato , Baldazzi Gianandrea , Catarci Marco , Ciaccio Giovanni , Garulli Gianluca , Pavanello Maurizio , Attinà Grazia Maria , Ricciardelli Luigi , Cuoghi Manuela , Azzinnaro Antonio , Castaldo Pasquale , Ciano Paolo , Lombari Pietro , Motter Michele , Giordano Alessio , Scatizzi Marco , Marini Pierluigi , Basti Massimo , Borghi Felice , Luridiana Gianluigi , Bottino Vincenzo , Cillara Nicola
Published: December 2024

Background:

Colorectal cancer (CRC) is a leading cause of cancer-related mortality worldwide. Despite advancements in surgical techniques and perioperative care, patient outcomes vary significantly across healthcare institutions. Textbook outcome (TO), a composite metric representing an ideal postoperative course, has been proposed as a standard for assessing the quality of surgical care in CRC. However, its impact on patient outcomes remains underexplored, particularly across diverse clinical settings.

Objective:

This study aims to explore surgeons’ adherence to TO criteria and identify patient-specific and procedural risk factors associated with TO failure. The study will also evaluate TO as a quality metric in CRC surgery, examining its association with short-term and long-term clinical outcomes in a multicenter cohort.

Methods:

This multicenter, retrospective cohort study will include all adult patients undergoing CRC resection between 1 January 2022 and 31 December 2024 across multiple centers in Italy, on behalf of the Italian Surgical Association (ACOI, Associazione Chirurghi Ospedalieri Italiani). The study will collect and analyze demographic, clinical, and surgical data to determine TO incidence and its association with key outcomes, including radical resection, 30-day mortality, morbidity, no reintervention, no ostomy placement, and a hospital stay of 14 days or less.

Conclusions:

This study will offer valuable insights into the utility of TO as a metric for evaluating the quality of care in CRC surgery. These findings may inform future guidelines and policies aimed at improving CRC surgical outcomes.
Absorbable gelatin sponge as an intrascleral buckle in rabbits: a pilot study
Authors: Zhou Yan , Lin Shiqun , Xiao Xingyu , Chen Youxin , Chen Zhe , Dai Rongping
Published: December 2024

Purpose:

This study aimed to evaluate the efficacy and safety of using an absorbable gelatin sponge as an intrascleral buckle in rabbit eyes; it also monitored degradation of the gelatin sponge over time.

Methods:

Ten New Zealand white rabbits underwent surgery to implant an absorbable gelatin sponge as an intrascleral buckle. Weekly ophthalmic examinations were conducted before and after the procedure until the implant was fully absorbed. Assessments included external eye and fundus examinations, color fundus imaging, and optical coherence tomography. Safety and efficacy were determined by comparing pre-operative and post-operative conditions.

Results:

The surgery was successfully completed in 12 of 20 eyes, yielding favorable postoperative outcomes. Eight eyes were excluded due to issues with scleral tunneling, including accidental penetration, suprachoroidal implantation of the sponge, and choroidal excavation, resulting in a success rate of 60%. The indentation produced by the gelatin sponge implant progressively decreased, entirely disappearing within 2 weeks. No complications, such as retinal or choroidal hemorrhage or detachment, were observed.

Conclusion:

Intrascleral implantation of absorbable gelatin sponge was safe and effective for scleral buckling in rabbits, demonstrating favorable biodegradation characteristics.
Evaluation of Foveal Hypoplasia in Children with a History of Retinopathy of Prematurity
Authors: Çelik Gökhan , Oto Bilge Batu , Kızılay Osman , Gunay Murat
Published: December 2024

Purpose:

To evaluate the foveal development in patients diagnosed with retinopathy of prematurity (ROP) and to evaluate whether foveal development was affected by treatment in ROP patients.

Methods:

This cross-sectional study included patients with a history of ROP. Foveal development was compared between eyes with spontaneous regression and treated eyes. Additionally, gestational age, birth weight, ROP zone and stage, and postmenstrual gestational age at the time of treatment, were evaluated. The final visual acuity was analyzed according to the foveal hypoplasia (FH) severity.

Results:

This study included 166 eyes from 83 patients. Foveal development was significantly different among the treatment and spontaneous regression groups, and FH was more severe in the treatment group. The prevalence of normal foveal development was higher in the spontaneous regression group than in the treatment groups. This suggests that ROP treatment may induce morphological alterations during foveal development. Gestational age, postmenstrual age at the time of treatment, ROP stage, and ROP zone were correlated with FH severity. Visual acuity was not affected by mild FH, and 88.5% of the patients had a visual acuity of LogMAR 0.

Conclusion:

Early stage foveal development is not significantly disrupted in patients with ROP, and patients with ROP show no significant visual disturbance associated with FH. However,eyes treated for ROP either with laser photocoagulation or intravitreal anti-vascular endothelial growth factor demonstrated more severe hypoplasia compared to that with spontaneous regression.
Machine Learning–based Prediction of Blood Stream Infection in Pediatric Febrile Neutropenia
Authors: Park Jun Sung , Song Jongkeon , Yoo Reenar , Kim Dahyun , Chun Min Kyo , Han Jeeho , Lee Jeong-Yong , Choi Seung Jun , Lee Jong Seung , Ryu Jeong-Min , Kang Sung Han , Koh Kyung-Nam , Im Ho Joon , Kim Hyery
Published: December 2024

Objectives:

This study aimed to develop machine learning (ML) prediction models for identifying bloodstream infection (BSI) and septic shock (SS) in pediatric patients with cancer who presenting febrile neutropenia (FN) at emergency department (ED) visit.

Materials and Methods:

A retrospective study was conducted on patients, younger than 18 years of age, who visited a tertiary university-affiliated hospital ED due to FN between January 2004 and August 2022. ML models, based on XGBoost, were developed for BSI and SS prediction.

Results:

After applying the exclusion criteria, we identified 4423 FN events during the study period. We identified 195 (4.4%) BSI and 107 (2.4%) SS events. The BSI and SS models demonstrated promising performance, with area under the receiver operating characteristic curve values of 0.87 and 0.88, respectively, which were superior to those of the logistic regression models. Clinical features, including body temperature, some laboratory results, vital signs, and diagnosis of acute myeloblastic leukemia were identified as significant predictors.

Conclusions:

The ML-based prediction models, which use data obtainable at ED visits may be valuable tools for ED physicians to predict BSI or SS.
The Impact of Unilateral Transfemoral Amputation on Lumbar Bone and Muscle Quality
Authors: Levy Hannah A. , Ulrich Marisa N. , Messer Caden , Pumford Andrew , Kelley Brian , Rose Peter S. , Currier Bradford , Nassr Ahmad N. , Freedman Brett A. , Helgeson Melvin , Houdek Matthew , Smither Fantley , Karamian Brian A. , Sebastian Arjun S.
Published: December 2024

Objective

To examine the long-term perioperative changes in lumbar bone density, muscle size and fatty atrophy, and facet degeneration after transfemoral amputation (TFA).

Design

All patients who underwent TFA at an academic center between 2002-2022 were retrospectively identified. Patients were required to have preoperative and postoperative CT (>1 year) and regularly utilize a prosthesis. Preoperative to postoperative changes in lumbar and muscular vertebral Hounsfield units (HU), facet degeneration, and bilateral psoas, quadratus lumborum, multifidus, and erector spinae cross-sectional area (CSA) were determined.

Results

A total of 42 patients met the inclusion criteria. There were significant preoperative to postoperative decreases in HUs in the L1 and L3 vertebral bodies were -17.69 and -25.35, respectively. There were significant pre- to post-operative increases in L4-5 and L5-S1 facet degeneration grade. There were significant pre- to post-operative decreases in amputated side psoas HU and CSA. There were also significant pre- to post-operative HU decreases in the bilateral multifidus and erector spinae muscles, where the changes were more pronounced on the contralateral side.

Conclusion

TFA was associated with progression of lumbar facet degeneration, small scale decreases in lumbar bone quality, amputated side psoas atrophy, and bilateral fatty infiltration of the multifidus and erector spinae.
The Effectiveness of Early Treatment With Intense Pulsed Light Combined With Fractional Erbium Laser in Preventing Post-traumatic Hypertrophic Scar Formation
Authors: Dai Qiang , Cheng Lin , Wang Cheng
Published: December 2024

Background:

Once scars form and begin to proliferate, treatment becomes challenging. Traditional methods of scar treatment often provide suboptimal results. Therefore, early intervention has become widely accepted, with a focus on prevention during the wound-healing phase rather than later treatment. Here, the authors evaluate the effectiveness of early treatment with intense pulsed light (IPL) combined with fractional erbium laser in preventing the formation of post-traumatic hypertrophic scars.

Methods:

A total of 120 patients who underwent emergency cosmetic suture surgery for facial trauma between January 2019 and December 2021 were selected for the study. The control group received conventional antiscar therapy (pressure therapy or antiscar medication), while the observation group received IPL combined with fractional erbium laser in addition to the conventional treatment. The specific treatment doses were adjusted based on the patient’s age, scar color, texture, and thickness. A treatment course consisted of 3 to 5 sessions, with 4-week intervals between treatments. Follow-up was conducted within 1 year after treatment to assess the improvement in scar appearance before and after therapy.

Results:

After IPL combined with fractional erbium laser treatment, patients in the observation group showed significantly lower scores in color, thickness, vascular distribution, softness, and total scores on the Vancouver Scar Scale (VSS) compared with the control group. During the follow-up, 3 complications were observed: 2 cases of skin blisters and 1 case of pigmentation. No immediate skin lesions, depigmentation, infections, ulcers, or other adverse reactions were reported.

Conclusions:

For patients with early-stage superficial scars following trauma surgery, early treatment with IPL combined with fractional erbium laser not only leads to significant improvements in appearance and effectively prevents hypertrophic scar formation but also promotes rapid recovery with few complications. This approach has clinical value.
Scoping Review of Ethical Discourse in Global Cleft Surgery Literature
Authors: Shamim Abrar , Ming Neil , Choi Ju Yeon , Seo Ga Young , Khalili Tali , Brady Noah , Wu Anette
Published: December 2024

Background:

The ethical discourse regarding the delivery of global surgical care has increased in the 21st century. The aims of this manuscript are to explore the differences in ethical domains in the global cleft surgical literature discussed by authors from high-income countries versus lower-middle-income countries and to elucidate changes in ethical discussions over the last decade.

Methods:

A thematic coding analysis was completed using NVivo 12 qualitative data analysis software. Articles were analyzed and coded for discussion of 24 distinct subdomains in the global cleft surgical literature from 1992 to 2022.

Findings:

The domains with the most significant discourse in the global cleft surgery literature found were (1) clinical care and delivery and (2) engagement in collaborations and partnerships. Furthermore, when manuscripts are first authored by low- and middle-income country (LMIC) authors, the subdomains of (1) level of visiting trainee supervision, (2) relevance of educational activities, and (3) patient/procedure/location selection increase in relative discourse. The impact of visiting trainees on local educational programs is the ethical subdomain that has the largest increase in the last decade. There are barriers to publication as evidenced by the exclusion of abstracts which included LMIC authors but did not result in publications in peer-reviewed journals.

Conclusions:

A critical finding of this study is that the distribution of discussed ethical domains differs when LMIC authors are included as authors, in particular when primary authorship is from an LMIC author. To the authors' knowledge, there is no other study to date which has attempted this form of analysis.
Application of 3D-Printed External Cranial Protection in the Treatment of Contralateral Subdural Effusion After Decompressive Craniectomy: A Technical Note
Authors: Sun Zhixiang , Fei Xi-feng , He Bao , Shi Lei , Cai Shizhong , Qian Jin
Published: December 2024

This technical note introduces the application of a 3D-printed external cranial protection device for contralateral subdural effusion after decompressive craniectomy (CSEDC). By applying this device over the cranial defect, the authors observed significant effects in reducing CSEDC formation, alleviating midline shift, and promoting neurological recovery. This report details the design and manufacturing process and presents comparative computed tomography images of a representative patient to demonstrate its efficacy.
Impact of obesity on low density lipoprotein plasmatic levels 6 weeks after an acute coronary syndrome
Authors: Bourgeois Elise , Benchalkha Daylale , Brobst Morgane , Herman Fanchon , Molinari Nicolas , Breuker Cyril , Chapet Nicolas , Roubille François , Sultan Ariane
Published: December 2024

Introduction

Cardiovascular disease is the leading cause of death. One of the main factors is obesity, which is on the rise. LDL levels below 0.55 g/L are recommended after ACS. To date, there are no specific recommendations for obese subjects.

Objective

The primary objective was to assess the impact of obesity on LDL-c target attainment 6 weeks after initiation of statin therapy in subjects admitted for ACS. The secondary objectives were to assess the evolution of cholesterol levels and to characterize lipid-lowering treatments.

Methods

The single-center observational study took place at Montpellier University Hospital and included patients admitted to the ICU for ACS not treated with statins (T0). Biological tests were performed at 6 weeks. At 3 months, a telephone call was made by two pharmacists to collect the results of their biological work-up and any therapeutic modifications.

Results

The results were analyzed on 286 patients. A total of 39.5% were overweight and 22.7% obese. After hospitalization, 95.4% were prescribed statins. At 6 weeks, LDL cholesterol averaged 1.58 mmol/L, lower in subjects with a BMI greater than 30 kg/m2 (1.32 mmol/L). On average, 49.46% of subjects reached the LDL cholesterol target, with obese subjects achieving a higher rate of 64.9%. There was no significant difference in the prescription of lipid-lowering treatments between the two groups.

Conclusion

Despite high-intensity statin prescription, the target was achieved by 67.6% of obese subjects and 44.8% of subjects with a BMI of less than 30 kg/m2. This shows that post-SCA management needs to be reinforced for the general population.
Quantification of Pseudomonas aeruginosa biofilms using electrochemical methods
Authors: Riordan Lily , Lasserre Perrine , Corrigan Damion , Duncan Katherine R
Published: December 2024

Currently 2.29% of deaths worldwide are caused by antimicrobial resistance (AMR), compared to 1.16% from malaria, and 1.55% from human immunodeficiency virus and acquired immunodeficiency syndrome (HIV/AIDs). Furthermore, deaths resulting from AMR are projected to increase to more than 10 million per annum by 2050. Biofilms are common in hospital settings, such as medical implants and pose a particular problem as they have shown resistance to antibiotics up to 1000-fold higher than planktonic cells because of dormant states and reduced growth rates. This is compounded by the fact that many antibiotics target mechanisms of active metabolism and are therefore less effective. The work presented here aimed to develop a method for biofilm quantification which could be translated into the clinical setting, as well as used in the screening of antibiofilm agents. This was carried out alongside crystal violet staining, as a published point of reference. Using electrochemical impedance spectroscopy and square wave voltammetry, P. aeruginosa biofilm formation was detected within an hour after seeding P. aeruginosa on the sensor. A 40% decrease in impedance modulus was shown when P. aeruginosa biofilm had formed, compared to the media only control. As such, this work offers a starting point for the development of real-time biofilm sensing technologies, which can be translated into implantable materials.
Unveiling the Ecology ofLegionellain a Stratified Freshwater Lake: Seasonal Dynamics, Host Interactions, and Persistence Under Oxygen Limited Conditions
Authors: Berman O. , Be’eri-Shlevin Y. , Ninio S.
Published: December 2024

Background

Legionellaare predominantly recognized as aerobic pathogens in man-made water systems. However, their potential persistence in natural freshwater environments, particularly under oxygen limited conditions, remains poorly explored. In this study we investigated the spatio-temporal dynamics ofLegionellaoccurrence in a seasonally stratified sub-tropical freshwater lake, with a focus on anaerobic conditions of the anoxic hypolimnion.

Results

Our study reveals significant seasonal variations inLegionellaabsolute abundance, with the highest concentrations occurring during and immediately following lake mixing events. Unexpectedly, high levels ofLegionellawere measured in the anaerobic hypolimnion layer of the lake. Utilizing genus specific amplicon-based sequencing, we found significant shifts inLegionellacommunity composition, that are related to the sampling month. Several environmental factors were associated with the observed changes, including temperature, DO, chlorophyll and dinoflagellate biomass. Moreover, we identifiedLegionellagenotypes unique to samples presenting hypoxic conditions - that were not closely related to knownLegionellaspecies. In addition, we noted genotypes present in anoxic samples, that were absent from the oxic layers of the corresponding sampling dates. These results were accompanied by changes in the interaction patterns betweenLegionellaand their potential hosts, in oxic and anoxic conditions.

Conclusions

This study challenges the conventional view ofLegionellaas a strictly aerobic pathogen by demonstrating its persistence in anoxic freshwater environments. Our findings suggest that certainLegionellaspecies may have adapted to low- oxygen conditions, potentially through alternate metabolic pathways or by residing within protozoan hosts. The identification of uniqueLegionellagenotypes in the hypolimnion, along with shifts in occurrence, diversity, and host interactions, underscores the complexity ofLegionellaecology. These results highlight the need for further research onLegionellain natural freshwater systems, which serve as reservoirs for the bacteria and potential sources for human infection. Further investigation into the mechanisms underlyingLegionellapersistence in anaerobic conditions and its interactions with environmental hosts is essential for a better understanding of the evolutionary forces shaping this family of human pathogens.
RpiBeh: a multi-purpose open-source solution for real-time tracking and behavior-driven closed-loop interventions in rodent neuroethology
Authors: Sun Yiqi , Zhang Jie , Wang Qianyun , Ni Jianguang
Published: December 2024

High-precision behavior tracking and closed-loop intervention are essential for studying the neural basis of cognition and behavior. Existing commercial systems are costly and inflexible for customization, while current open-source tools are often lack of real-time functionality and suffer from steep learning curve. To address these issues, we developed RpiBeh, an open-source, cost-effective, and versatile software tailored for rodent neuroethological research. The software features an intuitive interface with extensive customization options. RpiBeh leverages a Raspberry Pi and camera for video streaming, enabling behavior-driven closed-loop control. Additionally, it provides frame-by-frame video timestamp output for precise synchronization with external devices. For real-time tracking and locomotion pattern analysis, RpiBeh utilizes several novel algorithms and integrated newly developed deep-learning method. Specifically, we introduced two algorithms: a Background Subtraction Method (BSM) for real-time position tracking and a Frame Difference (FD) algorithm for freezing behavior detection. RpiBeh was validated in single animal real-time tracking and locomotion pattern detection, demonstrating flexibility and effectiveness in configurating behavior-triggered closed-loop reinforcement experiments including passive place avoidance task and social fear conditioning tasks. It achieved the same level of performance in tracking and locomotion pattern detection comparing to benchmark software including ANY-maze and DeepLabCut, with superior customization and expandability. Consequently, RpiBeh offers an efficient, affordable, and open-source solution for video tracking and behavior-driven closed-loop experiments.
From Pigments to Precision: Exploring Genetic Transformation and Genome Editing in Wheat and Barley
Authors: Prusty Manas Ranjan , Shatil-Cohen Arava , Kumar Rakesh , Sharma Davinder , Minz-Dub Anna , Ezrati Smadar , Hihinashvili Avigail , Sharon Amir
Published: December 2024

Genetic engineering of wheat is complex due to its large genome size, the presence of numerous genes with high sequence similarities, and a multitude of repetitive elements. In addition, genetic transformation of wheat has been difficult, mainly due to poor regeneration in tissue cultures. Recent advances in plant biotechnology, particularly the use of the regenerative genes GROWTH-REGULATING FACTOR (GRF) and GRF-INTERACTING FACTOR (GIF), have provided new tools for wheat transformation and regeneration. Another transformative tool is the RUBY system, that involves genetic engineering of three betalain biosynthesis genes, providing a noninvasive, visually detectable red pigment. In this study, we used theGRF4-GIF1chimera along with the RUBY system to advance transformation and gene editing in wheat and barley. The GRF4-GIF1 chimera significantly aided wheat regeneration; however, it had an opposite effect in barley, where it inhibited the regeneration process. Therefore, we primarily generated RUBY transgenic barley lines using constructs that did not include the GRF4-GIF1 chimera. Additionally, we used the RUBY cassette for fast assessment of gene editing by knockingout the first betalain biosynthetic gene in RUBY-positive transgenic wheat plants, resulting in a change of leaf color from red to green. The edited RUBY wheat lines lost more than just the red color. They also lost betalain-related traits, such as being less likely to get leaf rust (Puccinia triticina) and salt stress. Importantly, the loss of RUBY did not affect plant viability, making it a useful tool for genome editing and a viable alternative to destructive methods.
Hybridogenetic reproduction ofPelophylaxwater frogs from different R-E hemiclonal population systems from Eastern Ukraine: selective mortality, clonal and ploidy diversity
Authors: Fedorova Anna , Pustovalova Eleonora , Drohvalenko Mykola , Biriuk Olha , Doležálková-Kaštánková Marie , Kravchenko Maryna , Korshunov Olexii , Mikulíček Peter , Choleva Lukáš , Holovnia Dmytro , Dedukh Dmitrij , Shabanov Dmytro
Published: December 2024

European water frogs from thePelophylax esculentuscomplex include two sexual species,P. ridibundusandP. lessonae,and their hybrids, which usually clonally transmit one of the parental species’ genomes. This unique reproductive strategy allows hybrids to reproduce with one or both parental species, creating diverse population systems. Unlike most well-studied population systems in Europe, the Siverskyi Donets River basin in Eastern Ukraine features diploid and polyploid hybrids coexisting withP. ridibundus, whileP. lessonaeis absent (R-E systems). To reveal diverse system compositions, genetic divergence, and tadpole selective mortality, we combined novel data from over a decade of observations with previous research on population systems in the Siverskyi Donets River. Two main types of R-E systems were identified: those with diploid hybrids in northern localities and those with both diploid and triploid hybrids, extending from the mainstream of the Siverskyi Donets River to its tributaries. Additionally, we found higher genetic diversity in R-genomes compared to L-genomes, likely due to the absence ofP. lessonaeand the ongoing input of recombined R-genomes fromP. ridibundusand triploid hybrids. This study highlights the importance of continuous monitoring and research to unravel the dynamics and complexity of water frog population systems.
PRX-3140, a 5-HT4 Partial Agonist and Sigma-1 Agonist/Antagonist, Modulates Glucocorticoid Insulin Suppression and Cortisol Levels
Authors: Hood B.L. , McLaughlin J.P. , Alleyne A.R. , Thinschmidt J.S. , Harden S.W. , Frazier C.J. , Talton J.D.
Published: December 2024

PRX-3140 is a partial agonist to the 5-hydroxytryptamine receptor 4 (5-HT4) and a ligand for the sigma-1 (S1R) and sigma-2 (S2R) receptors. Although few publications have inferred S1R agonists/antagonists modulate blood glucose, Di et.al (2017) reported S1R deficiency in knockout mice impacted regulation of the hypothalamic-pituitary-adrenocortical (HPA) axis, with a dexamethasone-induced reduction in level of corticosterone markedly attenuated in S1R −/− knockout mice, implicating S1R in feedback response to the HPA axis. The hypothesis that S1R deficiency causes down-regulation of the glucocorticoid receptor (GR) and attenuates GR-mediated feedback inhibition of HPA axis, as well as stress response of HPA axis, suggest that the inverse, the activation of S1R under normal conditions, may modulate glucocorticoid insulin suppression (as a direct S1R-GR effect) as well as cortisol levels (producing HPA axis feedback inhibition). In the present study, coadministration of 10 µM PRX-3140 with 100 nM cortisol significantly increased insulin release (to 74.8 ng/ml, P-value <0.0001). Similar effects were observed when cells were exposed to dexamethasone (Dex), with 10 µM PRX-3140 and 10 nM Dex producing 1.87-fold significantly more insulin than 10 nM Dex alone. Daily glucose concentrations in the 14-day clinical study (NCT00384423) of PRX-3140 demonstrate a reduction for 10 mg once-daily at days 1, 7, 10, and 15. Urine free cortisol levels at 10, 30, 100 and 200 mg dose levels of PRX-3140 demonstrated a larger reduction at 7 and 14 days compared to placebo. As an agonist of S1R that acts as a chaperone of GR, PRX-3140 has demonstrated GR modulating effects in INS-1 cells and in 14-day clinical studies in healthy adults with low incidence of side effects. The results of the present study suggest that S1R activation, with PRX-3140 and NP-18-2 S1R agonists, modulates glucocorticoid insulin suppression and cortisol levels.
Development and validation of a real-time PCR assay for the diagnosis of rabies virus Philippine strain in non-brain samples
Authors: Manalo Daria L. , Bolivar Jude Karlo G. , Bondoc Jeromir G. , Nagataki Blanca J. , Nacion Leilanie B. , Espino Mark Joseph M. , Park Chun-Ho , Inoue Satoshi
Published: December 2024

Rabies is a fatal neurotropic and zoonotic disease responsible for thousands of deaths yearly. Direct fluorescent antibody test (dFAT), the gold standard in routine rabies diagnosis, requires dog brain samples, and takes 5-7 hours to obtain results. Brain specimen degradation due to inappropriate transport and storage conditions most of the time leads to false negative results, hence the need for an alternative diagnostic method that can also utilize non-brain specimens. In this study, an RT-qPCR assay was developed to specifically target the N gene of the Philippine rabies isolate. The assay was optimized using RNA from dFAT-positive dog brain tissues as templates. In-silico and in vitro evaluations both showed 100% specificity to rabies RNA, with a detection limit of 1 copy per microliter. Validation of the assay was done using dFAT-tested brain samples and potential brain specimen-alternates, specifically the dog nasal planum (NP) and follicle sinus complex (FSC). One hundred percent of the NP and FSC samples showed concordance with the respective dFAT-positive brain samples. Only 97% concordance was observed with the dFAT-negative brain samples. These results collectively validate the efficiency, sensitivity and specificity of the assay developed, indicating its potential utilization for in rabies diagnosis using clinical samples besides the brain tissues.
Significance of the CTP-binding motif for the interactions ofS. coelicolorParB with DNA, chromosome segregation, and sporogenic hyphal growth
Authors: Szymczak J. , Strzałka A. , Jakimowicz D. , Szafran MJ.
Published: December 2024

The segregation of bacterial chromosomes is widely mediated by partitioning proteins (ParAB). While ParB binds DNA specifically by recognising short, palindromic sequences known asparSsites, ParA utilises its ATPase activity to generate the force to translocate ParB-DNA nucleoprotein complexes (segrosomes). The assembly of the segrosome requires the association of ParB withparS,followed by nonspecific spread of the protein along the DNA. To spread on DNA, the ParB dimer must entrap theparSsite within the complex, a process triggered by CTP binding to the conserved GERR amino acid motif. InStreptomyces, a genus of soil-dwelling, multigenomic bacteria that have a complex life cycle, ParB-dependent chromosome partitioning is initiated during the growth of sporogenic hyphae. However, the molecular mechanisms underlying segrosome formation inStreptomycesand their ability to coordinate with sporogenic development remain incompletely understood.

In this study, we advance the understanding of chromosome segregation in bacteria by exploring the effects of CTP binding and hydrolysis on the formation of the partitioning complex inS. coelicolor. Here, viain vitroapproaches, we demonstrate that a conserved GERR motif is essential for CTP binding and hydrolysis byS. coelicolorParB. Moreover, the motif is crucial for CTP-dependent ParB accumulation on DNA. Using mutant strains, we show the significance of the GERR motif for segrosome complex assembly. Additionally, we provide data showing that the CTP-binding motif contributes to the regulation of the growth of sporogenic cells. Overall, we show that CTP-dependent segrosome assembly impacts the development ofS. coelicolorsporogenic cells.
Optimizing a Human Monoclonal Antibody for Better Neutralization of SARS-CoV-2
Authors: Wang Qian , Guo Yicheng , Casner Ryan G. , Yu Jian , Nair Manoj S. , Ho Jerren , Reddem Eswar R. , Tzang Chih Chen , Huang Yaoxing , Shapiro Lawrence , Liu Lihong , Ho David D.
Published: December 2024

SARS-CoV-2 has largely evolved to resist antibody pressure, with each successive viral variant becoming more and more resistant to serum antibodies in the population. This evolution has rendered inactive all therapeutic monoclonal antibodies previously authorized, and it is now threatening the remaining clinical product for immunoprophylaxis against COVID-19. We report herein the isolation of a human monoclonal antibody with a broad but incomplete SARS-CoV-2 neutralization profile, but structural analyses and mutational scanning led to the engineering of variants that resulted in greater antibody flexibility while binding to the viral spike. Three such optimized monoclonal antibodies neutralized all SARS-CoV-2 strains tested with much improved potency and breadth, including against subvariants KP.3.1.1 and XEC that are dominant today. The findings of this study not only present new antibody candidates for clinical development against COVID-19, but also introduce a unique engineering approach to improve antibody activity via increasing conformational flexibility.
DynaMAP: Dynamic Microbiome Abundance Profiling through high density optical mapping
Authors: Abakumov Sergey , Ruppeka-Rupeika Elizabete , Chen Xiong , Engelbrecht Mattias , Mestdagh Inge , D’huys Thomas , Mlodzinska Agata , Leen Volker , Szymanek Agata , Badola Aditya , Lukes Tomas , Demuyser Thomas , Hofkens Johan , Dedecker Peter , Bouwens Arno
Published: December 2024

Microbial abundance profiling is rapidly becoming an essential method in biomedical research, though it is often costly and time intensive. We present DynaMAP, a rapid approach for microbiome profiling that uses single-molecule imaging to develop an optical map of metagenomic DNA. DynaMAP achieves strain-level taxonomic profiling without requiring base-by-base sequencing and with a one-day turnaround time. In doing so, it delivers microbiome profiling that is comparable to shotgun sequencing but operates more efficiently, strongly expanding the possibility for microbiome analysis.
Divergence in poxvirus-encoded E3-like proteins can dictate poxvirus activation of cellular necroptosis
Authors: Enow Junior A. , Munig Saige , Sample Mathew L. , Speyer Gil , Chandrakanth Raghavi , Williams Jacqueline , Bonner James , McFadden Grant , Jacobs Bertram , Rahman Masmudur M.
Published: December 2024

Poxviruses encode a plethora of proteins to modulate diverse cellular responses against viruses. Poxvirus-encoded E3-like proteins are multifunctional, regulating diverse cellular antiviral responses. The canonical Vaccinia E3-like proteins have two domains: an N-terminal Z-form nucleic acid binding domain (Zα-BD) and a C-terminal double-stranded RNA binding domain (dsRNA-BD)-.Using protein sequence and structural homology modeling, we identified the presence of dsRNA- BD-containing proteins in all the poxviruses except Avipoxviruses, Salmon poxvirus and Entemopoxviruses. However, the acquisition of these proteins likely happened under three distinct events. Using structural homology modeling and FATCAT score, we can classify E3-like proteins in three distinct categories: i) the E3-like proteins with highly conserved dsRNA-BD but with or without the N-terminal domain, present in most poxviruses; ii) unconventional E3-like proteins with highly diverged dsRNA-BD, present in Macropoxvirus and Molluscipoxvirus and iii) E3-like protein with dsRNA-BD that may have different origin present in Crocodilepoxvirus.12–52–6

Members of Leporipoxvirus, Waddenpoxvirus, Cetaceanpoxvirus, and selected members of Orthopoxvirus contain E3-like proteins missing the N-terminal Zα-BD required for necroptosis inhibition. Additionally, using Alphafold, we show that the Zα-BD of Chordopoxviruses E3-like proteins is structurally more variable than the ds-RNA binding domain. Compared to members of Orthopoxviruses–Vaccinia virus (VACV) and Cowpox virus (CPXV) that have been shown to inhibit necroptosis and contain an N-terminus Zα-BD of the canonical E3 protein, our results show that members of leporipoxviruses induce necroptosis in human and mouse necroptosis competent cell lines. Furthermore, myxoma virus (MYXV) infection activates RIP1 and RIP3-mediated necroptosis in both human and mouse necroptosis-competent cells. These data suggest that Leporipoxviruses lack countermeasures to necroptosis compared to Orthopoxviruses that encode multiple key regulators of necroptosis, possibly due to a lack of selective pressure within the viral host species (Lagomorphs).

Graphical Abstract
Xenon photoionization in the vicinity of
4d
giant resonance and Cooper minimum using an XUV-NIR pump-probe experiment
Authors: Kumar Sonu , Düsterer Stefan , Frühling Ulrike , Alisauskas Skirmantas , Cirmi Giovanni , Kristin Czwalinna Marie , Große-Wortmann Uwe , Kschuev Nick , Kuschewski Frederik , Lang Tino , Lindenblatt Hannes , Manschwetus Bastian , Meister Severin , Papadopoulou Christina C. , Passow Christopher , Rönsch-Schulenburg Juliane , Schirmel Nora , Schulz Sebastian , Trost Florian , Xu Han , Litvinyuk Igor , Moshammer Robert , Kabachnik Nikolay M. , Erk Benjamin , Tul-Noor Atia
Published: December 2024

The relaxation processes in atomic xenon following core ionization of the 4d and 4p subshells by extreme ultraviolet (XUV) pulses from a free-electron laser (FLASH) are investigated using ion time-of-flight spectroscopy. We compare the dynamics following ionization and Auger-Meitner decays at 90-eV photon energy, i.e., near the giant resonance, with those at 160 eV, near the Cooper minimum, where cross sections for photoionization of the 4d and 4p subshells are similar. Final states with charges higher than 4 show signatures of sequential absorption of two XUV photons, followed by subsequent Auger-Meitner decay. The averaged lifetimes of some important excited states are measured in a two-color XUV-pump–near-infrared-probe experiment. A transient enhancement in the ion yield of Xe5+ with an average lifetime of (49±3) fs is obtained, attributed to transient intermediate states following the decay of 4d double-core-hole states.

Published by the American Physical Society
2024
Revisiting gauge invariance and Reggeization of pion exchange
Authors: Montaña Glòria , Winney Daniel , Bibrzycki Łukasz , Fernández-Ramírez César , Foti Giorgio , Hammoud Nadine , Mathieu Vincent , Perry Robert J. , Pilloni Alessandro , Rodas Arkaitz , Shastry Vanamali , Smith Wyatt A. , Szczepaniak Adam P. ,   Joint Physics Analysis Center Collaboration
Published: December 2024

The Reggeized pion is expected to provide the main contribution to the forward cross section in light meson photoproduction reactions with charge exchange at high energies. We discuss the Reggeization of pion exchange in charged pion photoproduction with an emphasis on consistency with current conservation. We show that the gauge-invariant amplitude for the exchange of a particle with a generic even spin J≥2 in the t channel is analytic at J=0 and that it can be interpreted in terms of the nucleon electric current. This enables us to reconcile the dynamics in the s and u channel, which involves also nucleon exchanges, with the amplitude expressed in terms of t-channel partial waves, as required by Regge theory.

Published by the American Physical Society
2024
Quantum Wire Coupled to Light
Authors: Bradley Victor , Sharma Kamal , Hafezi Mohammad , DeGottardi Wade
Published: December 2024

Experimental advances in cavity QED are raising the prospect of using light to probe quantum materials beyond the linear response regime. The capability to access quantum coherent phenomena would significantly advance the field. However, theoretical work on many-body systems coupled to light in the quantum coherent regime has been select. Here, we investigate the radiative properties of a finite-sized quantum wire in a microwave cavity. Examples of quantum wires include single-walled carbon nanotubes, a key experimental system in the field of nano-optics and plasmonics. We find that, for a variety of excited states, the repeated emission of photons results in the generation of many-body quantum entanglement. This leads to an increase in the rate at which subsequent photons are emitted, an example of Dicke superradiance. On the other hand, Pauli blocking tends to reduce this effect. Bosonization, the description of the excitations of a one-dimensional electron system as a gas of bosons, is found to be a powerful theoretical tool in this context. Its application means that many of our results generalize to wires with strong electron-electron interactions. The quantum wire thus represents a new platform to realize Dicke-model physics that does not rely on the various fine tunings necessary in traditional realizations involving many spatially isolated emitters. More broadly, this work demonstrates how quantum entanglement can be generated and measured in a many-body system.

Published by the American Physical Society
2024