bluuebunny/crossref_metadata_2025_split huggingface dataset:
Differences in the transcriptional immune response to Albugo candida between white rust resistant and susceptible cultivars in Brassica rapa L.
Authors: Miyaji Naomi , Akter Mst. Arjina , Shimizu Motoki , Mehraj Hasan , Doullah Md Asad-Ud , Dennis Elizabeth S. , Chuma Izumi , Fujimoto Ryo 
Published: May 2023

AbstractAlbugo candida causing white rust disease decreases the yield of Brassica rapa vegetables greatly. Resistant and susceptible cultivars in B. rapa vegetables have different immune responses against A. candida inoculation, however, the mechanism of how host plants respond to A. candida is still unknown. Using RNA-sequencing, we identified differentially expressed genes (DEGs) between A. candida inoculated [48 and 72 h after inoculation (HAI)] and non-inoculated samples in resistant and susceptible cultivars of komatsuna (B. rapa var. perviridis). Functional DEGs differed between the resistant and susceptible cultivars in A. candida inoculated samples. Salicylic acid (SA) responsive genes tended to be changed in their expression levels by A. candida inoculation in both resistant and susceptible cultivars, but different genes were identified in the two cultivars. SA-dependent systemic acquired resistance (SAR) involving genes were upregulated following A. candida inoculation in the resistant cultivar. Particular genes categorized as SAR that changed expression levels overlapped between A. candida and Fusarium oxysporum f. sp. conglutinans inoculated samples in resistant cultivar, suggesting a role for SAR in defense response to both pathogens particularly in the effector-triggered immunity downstream pathway. These findings will be useful for understanding white rust resistance mechanisms in B. rapa.
Microbial growth and adhesion of Escherichia coli in elastomeric silicone foams with commonly used additives
Authors: Rebane Ingrid , Priks Hans , Levin Karl Jakob , Sarigül İsmail , Mäeorg Uno , Johanson Urmas , Piirimägi Peeter , Tenson Tanel , Tamm Tarmo 
Published: May 2023

AbstractSilicone is often used in environments where water repellency is an advantage. Contact with water promotes the adhesion of microorganisms and biofilm formation. Depending on the application, this may increase the possibility of food poisoning and infections, the material's degrading appearance, and the likelihood of manufacturing defects. The prevention of microbial adhesion and biofilm formation is also essential for silicone-based elastomeric foams, which are used in direct contact with human bodies but are often difficult to clean. In this study, the microbial attachment in and the retention from the pores of silicone foams of different compositions is described and compared to those of commonly used polyurethane foams. The growth of the gram-negative Escherichia coli in the pores and their leaching during wash cycles is characterised by bacterial growth/inhibition, adhesion assay, and SEM imaging. The structural and surface properties of the materials are compared. Despite using common antibacterial additives, we have found that non-soluble particles stay isolated in the silicone elastomer layer, thus affecting surface microroughness. Water-soluble tannic acid dissolves into the medium and seems to aid in inhibiting planktonic bacterial growth, with a clear indication of the availability of tannic acid on the surfaces of SIFs.
Machine learning survival models trained on clinical data to identify high risk patients with hormone responsive HER2 negative breast cancer
Authors: Fanizzi Annarita , Pomarico Domenico , Rizzo Alessandro , Bove Samantha , Comes Maria Colomba , Didonna Vittorio , Giotta Francesco , La Forgia Daniele , Latorre Agnese , Pastena Maria Irene , Petruzzellis Nicole , Rinaldi Lucia , Tamborra Pasquale , Zito Alfredo , Lorusso Vito , Massafra Raffaella 
Published: May 2023

AbstractFor endocrine-positive Her2 negative breast cancer patients at an early stage, the benefit of adding chemotherapy to adjuvant endocrine therapy is not still confirmed. Several genomic tests are available on the market but are very expensive. Therefore, there is the urgent need to explore novel reliable and less expensive prognostic tools in this setting. In this paper, we shown a machine learning survival model to estimate Invasive Disease-Free Events trained on clinical and histological data commonly collected in clinical practice. We collected clinical and cytohistological outcomes of 145 patients referred to Istituto Tumori “Giovanni Paolo II”. Three machine learning survival models are compared with the Cox proportional hazards regression according to time-dependent performance metrics evaluated in cross-validation. The c-index at 10 years obtained by random survival forest, gradient boosting, and component-wise gradient boosting is stabled with or without feature selection at approximately 0.68 in average respect to 0.57 obtained to Cox model. Moreover, machine learning survival models have accurately discriminated low- and high-risk patients, and so a large group which can be spared additional chemotherapy to hormone therapy. The preliminary results obtained by including only clinical determinants are encouraging. The integrated use of data already collected in clinical practice for routine diagnostic investigations, if properly analyzed, can reduce time and costs of the genomic tests.
Specific mating behavior of Malayan pangolin (Manis javanica) in captivity
Authors: Yan Dingyu , Guo Xiaobing , Zeng Xiangyan , Jia Miaomiao , Tao Li , Wang Xiaoting , He Lun , Li Mingzhe , Guo Zhiming , Xu Shanghua , Li Baocai , Zeng Peng , Li Shousheng , Wei Yongjie 
Published: May 2023

AbstractPangolin is a mysterious animal in the Family Pholidota, Mammalia. Malayan pangolin (Manis javanica) is one of eight existing species and is listed in Manis. With the number of wild pangolins (Manis spp.) rapidly decreasing, captive breeding has become an important way to protect them from extinction. The research on mating behavior of pangolins is an important content to understand its reproductive characteristics and develop breeding management. From 2016 to 2022, a total of 360 mating events were observed in six males and 24 females through closed circuit television (CCTV) surveillance. The results show that males do not engage in complex courtship behavior before mating. In addition, we found that male pangolins adopted a ventrolateral mating position. Once males selected the side (left/right) of the female pangolin from which to approach to mate, they usually remained on the same side for subsequent mating, suggesting that male pangolins may have a preference in mating position. Finally, all mating events were observed at 1.72 ± 1.47 (n = 83, Mean ± SD) days after cohabitation and adjustment time before mating (from the male touching the female to intromission) took 4.98 ± 3.86 mins (n = 323). During mating, males hugged females and remained still for 47.37 ± 10.08 seconds (n = 323), which is the ejaculation and post-ejaculation quiescent time. Remarkably, we observed for the first time two peak mating times, 19:00 to 22:00 and 1:00 to 3:00, suggesting that they may have a preference for mating times. This study provides new insight into the mating behavior of M. javanica and contributes to the development of scientific conservation measures to improve the reproductive capacity of M. javanica.
A retrospective cohort study of incidence and risk factors for severe SARS-CoV-2 breakthrough infection among fully vaccinated people
Authors: Meister Tatjana , Kolde Anastassia , Fischer Krista , Pisarev Heti , Kolde Raivo , Kalda Ruth , Suija Kadri , Tisler Anna , Uusküla Anneli 
Published: May 2023

AbstractSARS-CoV-2 vaccination is currently the mainstay in combating the COVID-19 pandemic. However, there are still people among vaccinated individuals suffering from severe forms of the disease. We conducted a retrospective cohort study based on data from nationwide e-health databases. The study included 184,132 individuals who were SARS-CoV-2 infection-naive and had received at least a primary series of COVID-19 vaccination. The incidence of BTI (breakthrough infection) was 8.03 (95% CI [confidence interval] 7.95⎼8.13/10,000 person-days), and for severe COVID-19 it was 0.093 (95% CI 0.084⎼ 0.104/10,000 person-days). The protective effect of vaccination against severe COVID-19 remained constant for up to six months, and the booster dose offered an additional pronounced benefit (hospitalization aHR 0.32, 95% CI 0.19⎼0.54). The risk of severe COVID-19 was higher among those ≥ 50 years of age (aHR [adjusted hazard ratio] 2.06, 95% CI 1.25⎼3.42) and increased constantly with every decade of life. Male sex (aHR 1.32, 95% CI 1.16⎼1.45), CCI (The Charlson Comorbidity Index) score ≥ 1 (aHR 2.09, 95% CI 1.54⎼2.83), and a range of comorbidities were associated with an increased risk of COVID-19 hospitalization. There are identifiable subgroups of COVID-19-vaccinated individuals at high risk of hospitalization due to SARS-CoV-2 infection. This information is crucial to driving vaccination programs and planning treatment strategies.
Heterologous production of the D-cycloserine intermediate O-acetyl-L-serine in a human type II pulmonary cell model
Authors: Robbins Laurel , Balaram Ariane , Dejneka Stefanie , McMahon Matthew , Najibi Zarina , Pawlowicz Peter , Conrad William H. 
Published: May 2023

AbstractTuberculosis (TB) is the second leading cause of death by a single infectious disease behind COVID-19. Despite a century of effort, the current TB vaccine does not effectively prevent pulmonary TB, promote herd immunity, or prevent transmission. Therefore, alternative approaches are needed. We seek to develop a cell therapy that produces an effective antibiotic in response to TB infection. D-cycloserine (D-CS) is a second-line antibiotic for TB that inhibits bacterial cell wall synthesis. We have determined D-CS to be the optimal candidate for anti-TB cell therapy due to its effectiveness against TB, relatively short biosynthetic pathway, and its low-resistance incidence. The first committed step towards D-CS synthesis is catalyzed by the L-serine-O-acetyltransferase (DcsE) which converts L-serine and acetyl-CoA to O-acetyl-L-serine (L-OAS). To test if the D-CS pathway could be an effective prophylaxis for TB, we endeavored to express functional DcsE in A549 cells as a human pulmonary model. We observed DcsE-FLAG-GFP expression using fluorescence microscopy. DcsE purified from A549 cells catalyzed the synthesis of L-OAS as observed by HPLC–MS. Therefore, human cells synthesize functional DcsE capable of converting L-serine and acetyl-CoA to L-OAS demonstrating the first step towards D-CS production in human cells.
Deep ultraviolet fluorescence microscopy of three-dimensional structures in the mouse brain
Authors: Kasaragod Deepa Kamath , Aizawa Hidenori 
Published: May 2023

AbstractThree-dimensional (3D) imaging at cellular resolution improves our understanding of the brain architecture and is crucial for structural and functional integration as well as for the understanding of normal and pathological conditions in the brain. We developed a wide-field fluorescent microscope for 3D imaging of the brain structures using deep ultraviolet (DUV) light. This microscope allowed fluorescence imaging with optical sectioning due to the large absorption at the surface of the tissue and hence low tissue penetration of DUV light. Multiple channels of fluorophore signals were detected using single or a combination of dyes emitting fluorescence in the visible range of spectrum upon DUV excitation. Combination of this DUV microscope with microcontroller-based motorized stage enabled wide-field imaging of a coronal section of the cerebral hemisphere in mouse for deciphering cytoarchitecture of each substructure in detail. We extended this by integrating vibrating microtome which allowed serial block-face imaging of the brain structure such as the habenula in mouse. Acquired images were with resolution high enough for quantification of the cell numbers and density in the mouse habenula. Upon block-face imaging of the tissues covering entire extent of the cerebral hemisphere of the mouse brain, acquired data were registered and segmented for quantification of cell number in each brain regions. Results in the current analysis indicated that this novel microscope could be a convenient tool for large-scale 3D analysis of the brain in mice.
Targeted adaptive long-read sequencing for discovery of complex phased variants in inherited retinal disease patients
Authors: Nakamichi Kenji , Van Gelder Russell N. , Chao Jennifer R. , Mustafi Debarshi 
Published: May 2023

AbstractInherited retinal degenerations (IRDs) are a heterogeneous group of predominantly monogenic disorders with over 300 causative genes identified. Short-read exome sequencing is commonly used to genotypically diagnose patients with clinical features of IRDs, however, in up to 30% of patients with autosomal recessive IRDs, one or no disease-causing variants are identified. Furthermore, chromosomal maps cannot be reconstructed for allelic variant discovery with short-reads. Long-read genome sequencing can provide complete coverage of disease loci and a targeted approach can focus sequencing bandwidth to a genomic region of interest to provide increased depth and haplotype reconstruction to uncover cases of missing heritability. We demonstrate that targeted adaptive long-read sequencing on the Oxford Nanopore Technologies (ONT) platform of the USH2A gene from three probands in a family with the most common cause of the syndromic IRD, Usher Syndrome, resulted in greater than 12-fold target gene sequencing enrichment on average. This focused depth of sequencing allowed for haplotype reconstruction and phased variant identification. We further show that variants obtained from the haplotype-aware genotyping pipeline can be heuristically ranked to focus on potential pathogenic candidates without a priori knowledge of the disease-causing variants. Moreover, consideration of the variants unique to targeted long-read sequencing that are not covered by short-read technology demonstrated higher precision and F1 scores for variant discovery by long-read sequencing. This work establishes that targeted adaptive long-read sequencing can generate targeted, chromosome-phased data sets for identification of coding and non-coding disease-causing alleles in IRDs and can be applicable to other Mendelian diseases.
Hospital admissions and deaths due to acute cardiovascular events during the COVID-19 pandemic in residents of long-term care facilities
Authors: Gellert Paul , Kohl Raphael , Jürchott Kathrin , Noack Betty , Hering Christian , Gangnus Annabell , Steinhagen-Thiessen Elisabeth , Herrmann Wolfram J. , Kuhlmey Adelheid , Schwinger Antje 
Published: May 2023

AbstractHospital admissions due to acute cardiovascular events dropped during the COVID-19 pandemic in the general population; however, evidence for residents of long-term care facilities (LTCF) is sparse. We investigated rates of hospital admissions and deaths due to myocardial infarction (MI) and stroke in LTCF residents during the pandemic. Our nationwide cohort study used claims data. The sample comprised 1,140,139 AOK-ensured LTCF residents over 60 years of age (68.6% women; age 85.3 ± 8.5 years) from the largest statutory health insurance in Germany (AOK), which is not representative for all LTCF residents. We included MI and stroke admission and compared numbers of in-hospital deaths from January 2020 to end of April 2021 (i.e., during the first three waves of the pandemic) with the number of incidences in 2015–2019. To estimate incidence risk ratios (IRR), adjusted Poisson regression analyses were applied. During the observation period (2015–2021), there were 19,196 MI and 73,953 stroke admissions. MI admissions declined in the pandemic phase by 22.5% (IRR = 0.68 [CI 0.65–0.72]) compared to previous years. This decline was slightly more pronounced for NSTEMI than for STEMI. MI fatality risks remained comparable across years (IRR = 0.97 [CI95% 0.92–1.02]). Stroke admissions dropped by 15.1% (IRR = 0.75 [CI95% 0.72–0.78]) in the pandemic. There was an elevated case fatality risk for haemorrhagic stroke (IRR = 1.09 [CI95% 1.03–1.15]) but not for other stroke subtypes compared to previous years. This study provides first evidence of declines in MI and stroke admissions and in-hospital deaths among LTCF residents during the pandemic. The figures are alarming given the acute nature of the conditions and the vulnerability of the residents.
Occurrence and genetic diversity of prophage sequences identified in the genomes of L. casei group bacteria
Authors: Jarocki Piotr , Komoń-Janczara Elwira , Młodzińska Agata , Sadurski Jan , Kołodzińska Kinga , Łaczmański Łukasz , Panek Jacek , Frąc Magdalena 
Published: May 2023

AbstractIt is widely believed that microorganisms belonging toL. caseigroup can have positive effects on the human body. Therefore, these bacteria are used in many industrial processes, including the production of dietary supplements and probiotic preparations. When using live microorganisms in technological processes, it is important to use those without phage sequences within their genomes that can ultimately lead to lysis of the bacteria. It has been shown that many prophages have a benign nature, meaning that they don’t directly lead to lysis or inhibit microbial growth. Moreover, the presence of phage sequences in the genomes of these bacteria increases their genetic diversity, which may contribute to easier colonization of new ecological niches. In the 439 analyzed genomes of theL. caseigroup, 1509 sequences of prophage origin were detected. The average length of intact prophage sequences analyzed was just under 36 kb. GC content of tested sequences was similar for all analyzed species (44.6 ± 0.9%). Analyzing the protein coding sequences collectively, it was found that there was an average of 44 putative ORFs per genome, while the ORF density of all phage genomes varied from 0.5 to 2.1. The average nucleotide identity calculated on sequence alignments for analyzed sequences was 32.7%. Of the 56L. caseistrains used in the next part of the study, 32 did not show culture growth above the OD600 value of 0.5, even at a mitomycin C concentration of 0.25 μg/ml. Primers used for this study allowed for the detection of prophage sequences for over 90% of tested bacterial strains. Finally, prophages of selected strains were induced using mitomycin C, phage particles were isolated and then genomes of viruses obtained were sequenced and analyzed.
NXP032 ameliorates cognitive impairment by alleviating the neurovascular aging process in aged mouse brain
Authors: Lee Jae-Min , Lee Joo Hee , Kim So Hee , Sim Tae Hyeok , Kim Youn-Jung 
Published: May 2023

AbstractVascular aging is well known to be associated with the breakdown of the neurovascular unit (NVU), which is essential for maintaining brain homeostasis and linked to higher cognitive dysfunction. Oxidative stress is believed to be a significant cause of the vascular aging process. Vitamin C is easily oxidized under physiological conditions, so it loses its potent antioxidant activity. We developed a DNA aptamer that enhances the function of vitamin C. NXP032 is the binding form of the aptamer and vitamin C. In this study, we investigated the effect of NXP032 on neurovascular stabilization through the changes of PECAM-1, PDGFR-β, ZO-1, laminin, and glial cells involved in maintaining the integrity of the blood–brain barrier (BBB) in aged mice. NXP032 was orally administered daily for 8 weeks. Compared to young mice and NXP032-treated mice, 20-month-old mice displayed cognitive impairments in Y-maze and passive avoidance tests. NXP032 treatment contributed to reducing the BBB damage by attenuating the fragmentation of microvessels and reducing PDGFR-β, ZO-1, and laminin expression, thereby mitigating astrocytes and microglia activation during normal aging. Based on the results, we suggest that NXP032 reduces vascular aging and may be a novel intervention for aging-induced cognitive impairment.
A high-absorbance water-soluble photoinitiator nanoparticle for hydrogel 3D printing: synthesis, characterization and in vitro cytotoxicity study
Authors: Ghazali Hanieh Sadat , Askari Esfandyar , Seyfoori Amir , Naghib Seyed Morteza 
Published: May 2023

AbstractLight-based hydrogel crosslinking is a new approach in rapid and high-resolution 3D printing; however, using this method in tissue engineering is challenging due to the toxicity of photoinitiators, their solvents, and their low efficiency. Herein, a novel, water-soluble photoinitiator with high efficiency in light-based 3D printing is introduced. Low-cost photoinitator, 2,4,6-trimethylbenzoylphenyl phosphinate, is converted into nanoparticles via a microemulsion method and dispersed in water. Cell toxicity assays were performed to prove that these nanoparticles are non-toxic and can be used in biomedical applications. Finally, the nanoparticles were utilized in the high-accuracy 3D printing of hydrogels. The results of this study indicate that these particles are potent to be used in bioprinting.
Thalamocortical loops as temporal demodulators across senses
Authors: Ahissar Ehud , Nelinger Guy , Assa Eldad , Karp Ofer , Saraf-Sinik Inbar 
Published: May 2023

AbstractSensory information is coded in space and in time. The organization of neuronal activity in space maintains straightforward relationships with the spatial organization of the perceived environment. In contrast, the temporal organization of neuronal activity is not trivially related to external features due to sensor motion. Still, the temporal organization shares similar principles across sensory modalities. Likewise, thalamocortical circuits exhibit common features across senses. Focusing on touch, vision, and audition, we review their shared coding principles and suggest that thalamocortical systems include circuits that allow analogous recoding mechanisms in all three senses. These thalamocortical circuits constitute oscillations-based phase-locked loops, that translate temporally-coded sensory information to rate-coded cortical signals, signals that can integrate information across sensory and motor modalities. The loop also allows predictive locking to the onset of future modulations of the sensory signal. The paper thus suggests a theoretical framework in which a common thalamocortical mechanism implements temporal demodulation across senses.
Fatigue-driven compliance increase and collagen unravelling in mechanically tested anterior cruciate ligament
Authors: Putera Kevin H. , Kim Jinhee , Baek So Young , Schlecht Stephen H. , Beaulieu Mélanie L. , Haritos Victoria , Arruda Ellen M. , Ashton-Miller James A. , Wojtys Edward M. , Banaszak Holl Mark M. 
Published: May 2023

AbstractApproximately 300,000 anterior cruciate ligament (ACL) tears occur annually in the United States, half of which lead to the onset of knee osteoarthritis within 10 years of injury. Repetitive loading is known to result in fatigue damage of both ligament and tendon in the form of collagen unravelling, which can lead to structural failure. However, the relationship between tissue’s structural, compositional, and mechanical changes are poorly understood. Herein we show that repetitive submaximal loading of cadaver knees causes an increase in co-localised induction of collagen unravelling and tissue compliance, especially in regions of greater mineralisation at the ACL femoral enthesis. Upon 100 cycles of 4× bodyweight knee loading, the ACL exhibited greater unravelled collagen in highly mineralized regions across varying levels of stiffness domains as compared to unloaded controls. A decrease in the total area of the most rigid domain, and an increase in the total area of the most compliant domain was also found. The results highlight fatigue-driven changes in both protein structure and mechanics in the more mineralized regions of the ACL enthesis, a known site of clinical ACL failure. The results provide a starting point for designing studies to limit ligament overuse injury.