bluuebunny/crossref_metadata_2025_split huggingface dataset:
Suitability of microbial and organic matter indicators for on‐farm soil health monitoring
Authors: Huber Sabine , Bernardini Luca Giuliano , Bennett Alexandra , Fohrafellner Julia , Dohnke Katharina , Bieber Magdalena , Vuolo Francesco , Mentler Axel , Bodner Gernot , Keiblinger Katharina 
Published: November 2023

AbstractIn addition to standard laboratory testing of soil samples, on‐farm soil health monitoring methods are needed to help farmers assess progress in adopting new management practices. However, there is currently a lack of studies evaluating the suitability of semi‐quantitative on‐farm indicators to accurately rank target soil properties according to laboratory results. Therefore, this study assessed methods with potential for field use compared to common laboratory approaches for the determination of (i) soil organic carbon (SOC), (ii) carbon (C) fractions and (iii) microbial activity. The comparison allowed the evaluation of the validity, practicality and cost‐effectiveness of the approaches. For this purpose, three sites in north‐eastern Austria with contrasting soil textures (light, medium, heavy) and two different management systems (namely ‘pioneer’ and ‘standard’) were selected. Pioneer soils are managed long‐term according to principles of soil health using conservation agricultural practices while neighbouring fields under standard management represent conventional practices. Beyond texture and site differences, both laboratory and field‐adapted approaches revealed differences between the pioneer and standard systems. Overall, management‐specific differences were most pronounced in the light and heavy textured soil. Although the laboratory methods provided more accurate results with less variability, the field‐based approaches still identified trends in soil health parameters in the pioneer system. Our study can thus serve as a guide for the selection of suitable parameters and methods for assessing soil health in different areas of research and practical application.
Risk of severe coronavirus disease 2019 despite vaccination in patients requiring treatment with immune‐suppressive drugs: A nationwide cohort study of US Veterans
Authors: Anand Sonia T. , Vo Austin D. , La Jennifer , Brophy Mary , Do Nhan V. , Fillmore Nathanael R. , Branch‐Elliman Westyn , Monach Paul A. 
Published: November 2023

AbstractBackgroundPatients taking immune‐suppressive drugs are at increased risk of severe coronavirus disease 2019 (COVID‐19), not fully ameliorated by vaccination. We assessed the contributions of clinical and demographic factors to the risk of severe disease despite vaccination in patients taking immune‐suppressive medications for solid organ transplantation (SOT), rheumatoid arthritis (RA), inflammatory bowel disease (IBD), or psoriasis.MethodsVeterans Health Administration electronic health records were used to identify patients diagnosed with RA, IBD, psoriasis, or SOT who had been vaccinated against severe acute respiratory syndrome coronavirus 2, were subsequently infected, and had received immune‐suppressive drugs within 3 months before infection. The association of severe (defined as hypoxemia, mechanical ventilation, dexamethasone use, or death) versus non‐severe COVID‐19 with the use of immune‐suppressive and antiviral drugs and clinical covariates was assessed by multivariable logistic regression.ResultsSevere COVID‐19 was more common in patients with SOT (230/1011, 22.7%) than RA (173/1355, 12.8%), IBD (51/742, 6.9%), or psoriasis (82/1125, 7.3%). Age was strongly associated with severe COVID‐19, adjusted odds ratio (aOR) of 1.04 (CI 1.03–1.05) per year. Comorbidities indicating chronic brain, heart, lung, or kidney damage were also associated with severity, aOR 1.35–2.38. The use of glucocorticoids was associated with increased risk (aOR 1.66, CI 1.39–2.18). Treatment with antivirals was associated with reduced severity, for example, aOR 0.28 (CI 0.13–0.62) for nirmatrelvir/ritonavir.ConclusionThe risk of severe COVID‐19 despite vaccination is substantial in patients taking immune‐suppressive drugs, more so in patients with SOT than in patients with inflammatory diseases. Age and severe comorbidities contribute to risk, as in the general population. Oral antivirals were very beneficial but not widely used.
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Chromosomal‐scale genomes of two Rosa species provide insights into genome evolution and ascorbate accumulation
Authors: Zong Dan , Liu Huan , Gan Peihua , Ma Shaojie , Liang Hongping , Yu Jinde , Li Peilin , Jiang Tao , Sahu Sunil Kumar , Yang Qingqing , Zhang Deguo , Li Laigeng , Qiu Xu , Shao Wenwen , Yang Jinlong , Li Yonghe , Guang Xuanmin , He Chengzhong 
Published: November 2023

SUMMARYRosa roxburghii and Rosa sterilis, two species belonging to the Rosaceae family, are widespread in the southwest of China. These species have gained recognition for their remarkable abundance of ascorbate in their fresh fruits, making them an ideal vitamin C resource. In this study, we generated two high‐quality chromosome‐scale genome assemblies for R. roxburghii and R. sterilis, with genome sizes of 504 and 981.2 Mb, respectively. Notably, we present a haplotype‐resolved, chromosome‐scale assembly for diploid R. sterilis. Our results indicated that R. sterilis originated from the hybridization of R. roxburghii and R. longicuspis. Genome analysis revealed the absence of recent whole‐genome duplications in both species and identified a series of duplicated genes that possibly contributing to the accumulation of flavonoids. We identified two genes in the ascorbate synthesis pathway, GGP and GalLDH, that show signs of positive selection, along with high expression levels of GDP‐d‐mannose 3′, 5′‐epimerase (GME) and GDP‐l‐galactose phosphorylase (GGP) during fruit development. Furthermore, through co‐expression network analysis, we identified key hub genes (MYB5 and bZIP) that likely regulate genes in the ascorbate synthesis pathway, promoting ascorbate biosynthesis. Additionally, we observed the expansion of terpene synthase genes in these two species and tissue expression patterns, suggesting their involvement in terpenoid biosynthesis. Our research provides valuable insights into genome evolution and the molecular basis of the high concentration of ascorbate in these two Rosa species.
Sports Attitudes in Childhood and Income in Adulthood
Authors: Vanzella-Yang Adam , Domond Pascale , Vitaro Frank , Tremblay Richard E. , Bégin Vincent , Côté Sylvana 
Published: November 2023

Research shows that sports participation in youth is associated with earnings in adulthood. However, studies have often relied on self-reported earnings and on single indicators of sports participation. Using large-scale data linked to administrative records, we investigate: (a) whether sports attitudes at age 13 are uniquely related to income at ages 30–36 and (b) whether educational attainment and mental health in early adulthood mediate this association. We find that a one SD increase in sports attitudes is related to a 10% increase in income. This association is not entirely confounded by preexisting and co-occurring risk factors. Educational attainment mediates 22% of the association between sports attitudes and income. Sports attitudes are potentially a form of capital deployed in the pursuit of socioeconomic advantages.
Epidemiology and impact of methicillin-sensitive
Staphylococcus aureus
with β-lactam antibiotic inoculum effects in adults with cystic fibrosis
Authors: Svishchuk J. , Ebbert K. , Waddell B. , Izydorczyk C. , Acosta N. , Somayaji R. , Rabin H. R. , Bjornson C. L. , Lisboa L. , Gregson D. B. , Conly J. M. , Surette M. G. , Parkins M. D. 
Published: November 2023

ABSTRACT

Staphylococcus aureus
is the most prevalent cystic fibrosis (CF) pathogen. Several phenotypes are associated with worsened CF clinical outcomes including methicillin-resistance and small-colony-variants. The inoculum effect (IE) is characterized by reduced β-lactam susceptibility when assessed at high inoculum. The IE associates with worse outcomes in bacteremia and other high-density infections, and may therefore be relevant to CF. The prevalence of IE amongst a CF cohort (age ≥18 years), followed from 2013 to 2016, was investigated. Yearly methicillin-sensitive
S. aureus
(MSSA) isolates were screened at standard (5 × 10
5
CFU/mL) and high (5 × 10
7
CFU/mL) inoculum against narrow-spectrum anti-Staphylococcal β-lactams and those with anti-pseudomonal activity common to CF. A ≥ 4-fold increase in minimum inhibitory concentration between standard and high inoculum defined IE. Isolates underwent
blaZ
sequencing and genotyping and were compared against published genomes. Fifty-six percent (99/177) of individuals had MSSA infection. MSSA was observed at ≥10
5
CFU/mL in 44.8% of entry sputum samples. The prevalence of the IE was 25.0%-cefazolin; 13.5%-cloxacillin; 0%-meropenem; 1.0%-cefepime; 5.2%-ceftazidime; and 34.4%-piperacillin-tazobactam amongst baseline MSSA isolates assessed.
blaZ
A associated with cefazolin IE (
P
= 0.0011), whereas
blaZ
C associated with piperacillin-tazobactam IE (
P
< 0.0001). Baseline demographics did not reveal specific risk factors for IE-associated infections, nor were long-term outcomes different. Herein, we observed the IE in CF-derived MSSA disproportionally for cefazolin and piperacillin-tazobactam and this phenotype strongly associated with underlying
blaZ
genotype. The confirmation of CF being a high density infection, and the identification of high prevalence of MSSA with IE in CF supports the need for prospective pulmonary exacerbation treatment studies to understand the impact of this phenotype.
A preclinical model of TB meningitis to determine drug penetration and activity at the sites of disease
Authors: Lanni Faye , Antilus Sainte Rosleine , Hansen, Mark , Parigi Paul , Kaya Firat , LoMauro Katherine , Siow Bernard , Wilkinson Robert J. , Wasserman Sean , Podell Brendan K. , Gengenbacher Martin , Dartois Véronique 
Published: November 2023

ABSTRACT

Tuberculosis meningitis (TBM) is essentially treated with the first-line regimen used against pulmonary tuberculosis, with a prolonged continuation phase. However, clinical outcomes are poor in comparison, for reasons that are only partially understood, highlighting the need for improved preclinical tools to measure drug distribution and activity at the site of disease. A predictive animal model of TBM would also be of great value to prioritize promising drug regimens to be tested in clinical trials, given the healthy state of the development pipeline for the first time in decades. Here, we report the optimization of a rabbit model of TBM disease induced via inoculation of
Mycobacterium tuberculosis
into the cisterna magna, recapitulating features typical of clinical TBM: neurological deterioration within months post-infection, acid-fast bacilli in necrotic lesions in the brain and spinal cord, and elevated lactate levels in cerebrospinal fluid (CSF). None of the infected rabbits recovered or controlled the disease. We used young adult rabbits, the size of which allows for spatial drug quantitation in critical compartments of the central nervous system that cannot be collected in clinical studies. To illustrate the translational value of the model, we report the penetration of linezolid from plasma into the CSF, meninges, anatomically distinct brain areas, cervical spine, and lumbar spine. Across animals, we measured the bacterial burden concomitant with neurological deterioration, offering a useful readout for drug efficacy studies. The model thus forms the basis for building a preclinical platform to identify improved regimens and inform clinical trial design.
Experimental models for HIV latency and molecular tools for reservoir quantification—an update
Authors: Angamuthu Divyadarshini , Vivekanandan Sandhya , Hanna Luke Elizabeth 
Published: November 2023

SUMMARY

A major impediment for HIV cure is the ability of the virus to integrate its genome in the form of replication-competent proviral DNA into the cellular genome of the host and remain transcriptionally silent and hidden from the host’s immune defense mechanisms in latent reservoir cells. These latent reservoirs are highly heterogeneous, long-lived cells that are capable of reactivating to restore the viremic stage in virally suppressed individuals upon treatment interruption, thus necessitating life-long antiretroviral treatment. Latency reversal has become one of the most explored therapeutic approaches for eliminating HIV reservoirs and effecting HIV cure. Various aspects governing the establishment, maintenance, and reversal of HIV latency continue to be an enigma and warrant further research. Quantifying the size of the latent reservoir pool is also a challenge as these cells are very few in number and cannot be easily differentiated from uninfected cells. This article provides a comprehensive review of the
in vitro
and
in vivo
models currently available for studying HIV latency as well as the recently developed molecular tools for detection and quantification of latent viral reservoirs.
Multiantigen print immunoassay (MAPIA) for the diagnosis of neurocysticercosis: a single-center diagnostic optimization and accuracy study in Lima, Peru
Authors: Toribio L. , Guzman C. , Noazin S. , Zimic-Sheen A. , Zimic M. , Gonzales I. , Saavedra H. , Pretell E. J. , Bustos J. A. , Handali S. , García H. H. ,   on behalf of The Cysticercosis Working Group in Peru
Published: November 2023

ABSTRACT
Neurocysticercosis (NCC) is the most common helminthic infection of the human central nervous system. The antibody detection assay of choice is the enzyme-linked immunoelectrotransfer blot assay using lentil-lectin purified parasite antigens (LLGP-EITB, Western blot), an immunoassay with exceptional performance in clinical samples. However, its use is mainly restricted to a few research laboratories because the assay is labor-intensive and requires sophisticated equipment, expertise, and large amounts of parasite material for preparation of reagents. We report a new immunoprint assay (MAPIA) that overcomes most of these barriers. We initially compared the performance of five different antigen combinations in a subset of defined samples in the MAPIA format. After selecting the best-performing assay format (a combination of rGP50 + rT24H + sTs14 antigens), 148 archived serum samples were tested, including 40 from individuals with parenchymal NCC, 40 with subarachnoid NCC, and 68 healthy controls with no evidence of neurologic disease. MAPIA using three antigens (rGP50 + rT24H + sTs14) was highly sensitive and specific for detecting antibodies in NCC. It detected 39 out of 40 (97.5%) parenchymal NCC cases and 40/40 (100%) subarachnoid cases and was negative in 67 out of 68 (98.53%) negative samples. MAPIA using three recombinant and synthetic antigens is a simple and economical tool with a performance equivalent to the LLGP-EITB assay for the detection of specific antibodies to NCC. The MAPIA overcomes existing barriers to adoption of the EITG LLGP and is a candidate for worldwide use.
Developing a faculty support program for fostering enriching undergraduate laboratory experiences under limited resource conditions
Authors: Kulkarni Anuttama 
Published: November 2023

ABSTRACT
Meaningful pedagogical reform requires good faculty training and support programs. Such support is particularly valuable when colleges and universities are trying to bring research and inquiry into the laboratory curricula under resource-limited conditions. In this situation, it may help to extend the scope of the faculty support program to include training for practicing experimental techniques, sustainable networking opportunities, and a space to learn about pedagogical reforms. From this perspective, we share our experience about building a faculty development program for public college teachers who teach undergraduate biology in India. Though we designed the program for low-resource settings, the experiments curated could very well represent core biological concepts typically identified by the international community. The activities and overall design of the program can be useful for initiating pedagogical reform in any college/university where the traditional approach to biology laboratory instruction predominates, and high-end research is not easy to access.
Virus replication in the honey bee parasite,
Varroa destructor
Authors: Damayo James E. , McKee Rebecca C. , Buchmann Gabriele , Norton Amanda M. , Ashe Alyson , Remnant Emily J. 
Published: November 2023

ABSTRACT

The ectoparasitic mite
Varroa destructor
is the leading threat to the health of Western honey bees (
Apis mellifera
) primarily through its action as a vector of viruses. However, it is unclear which of the viruses transmitted by
V. destructor
actively infect and replicate in mites, which could facilitate increased transmission. To better understand the role of
V. destructor
as a vector, we took advantage of differences between bee and mite antiviral RNA interference pathways to identify the host specificity of replicating viruses. We used small RNA sequencing of individual
V. destructor
mites to examine viral small interfering RNA (vsiRNA) profiles of deformed wing virus genotypes (DWV-A and DWV-B), associated with colony declines, as well as nine other viruses present in our samples. We found active replication of six
V. destructor
-associated viruses, including a novel virus, Varroa destructor virus 9 (VDV-9), and replication of two honey bee-associated viruses, including both DWV-A and -B genotypes, confirming that mites are biological vectors for important bee pathogens. We show that the antiviral RNAi response can be used to define the host range of viruses in host-parasite interactions, such as honey bees and their parasites, enabling a better understanding of the role of a vector in the evolution and spread of honey bee pathogens.

IMPORTANCE

The parasitic mite
Varroa destructor
is a significant driver of worldwide colony losses of our most important commercial pollinator, the Western honey bee
Apis mellifera
. Declines in honey bee health are frequently attributed to the viruses that mites vector to honey bees, yet whether mites passively transmit viruses as a mechanical vector or actively participate in viral amplification and facilitate replication of honey bee viruses is debated. Our work investigating the antiviral RNA interference response in
V. destructor
demonstrates that key viruses associated with honey bee declines actively replicate in mites, indicating that they are biological vectors, and the host range of bee-associated viruses extends to their parasites, which could impact virus evolution, pathogenicity, and spread.
Identification of host essential factors for recombinant AAV transduction of the polarized human airway epithelium
Authors: Hao Siyuan , Zhang Xiujuan , Ning Kang , Feng Zehua , Park Soo Yeun , Aksu Kuz Cagla , McFarlin Shane , Richart Donovan , Cheng Fang , Zhang Elizabeth Yan , Zhang-Chen Aaron , Yan Ziying , Qiu Jianming 
Published: November 2023

ABSTRACT

Recombinant (r)AAV2.5T was selected from the directed evolution of an adeno-associated virus (AAV) capsid library in the human airway epithelium (HAE). The capsid gene of rAAV2.5T is a chimera of the N-terminal unique coding sequence of AAV2 VP1 unique (VP1u) and the VP2- and VP3-coding sequences of AAV5 with a single amino acid mutation of A581T. We conducted two rounds of genome-wide CRISPR guide (g)RNA library screening for host factors limiting rAAV2.5T transduction in HeLa S3 cells. The screening identified several genes that are critical for rAAV2.5T, including the previously reported genes
KIAA0319L
,
TM9SF2
,
VPS51
, and
VPS54
, as well as a novel gene
WDR63
. We verified the role of KIAA0319L and WDR63 in rAAV2.5T transduction of polarized HAE by utilizing CRISPR gene knockouts. Although KIAA0319L, a proteinaceous receptor for multiple AAV serotypes, played an essential role in rAAV2.5T transduction of polarized HAE either from the apical or basolateral side, our findings demonstrated that the internalization of rAAV2.5T was independent of KIAA0319L. Importantly, we confirmed that WDR63 is an important player in rAAV2.5T transduction of HAE while not being involved in vector internalization and nuclear entry. Furthermore, we identified that the basal stem cells of HAE can be significantly transduced by rAAV2.5T.

IMPORTANCE

The essential steps of successful gene delivery by recombinant adeno-associated viruses (rAAVs) include vector internalization, intracellular trafficking, nuclear import, uncoating, double-stranded (ds)DNA conversion, and transgene expression. rAAV2.5T has a chimeric capsid of AAV2 VP1u and AAV5 VP2 and VP3 with the mutation A581T. Our investigation revealed that KIAA0319L, the multiple AAV serotype receptor, is not essential for vector internalization but remains critical for efficient vector transduction to human airway epithelia. Additionally, we identified that a novel gene
WDR63
, whose cellular function is not well understood, plays an important role in vector transduction of human airway epithelia but not vector internalization and nuclear entry. Our study also discovered the substantial transduction potential of rAAV2.5T in basal stem cells of human airway epithelia, underscoring its utility in gene editing of human airways. Thus, the knowledge derived from this study holds promise for the advancement of gene therapy in the treatment of pulmonary genetic diseases.
Complete genome sequence of
Pseudomonas veronii
strain OST1911 isolated from oil sand tailing pond water in Alberta, Canada
Authors: Shideler Steven M. , Goff Kira , Gauthier Jeff , Levesque Roger C. , Lewenza Shawn 
Published: November 2023

ABSTRACT

Here, we report the complete genome sequence of
Pseudomonas veronii
strain OST1911, recovered from oil sand process-affected water accumulated in tailing ponds. This water contains numerous organic and inorganic compounds of environmental significance. The genome size is 6,435,955 bp with a G+C content of 61.21%.
Three novel sequencing types from seventeen
Staphylococcus aureus
genomes isolated from dairy cows milk in the Free State Province of South Africa
Authors: Khasapane Ntelekwane George , Kwenda Stanford , Khumalo Zamantungwa Thobeka Happiness , Nkhebenyane Sebolelo Jane , Thekisoe Oriel 
Published: November 2023

ABSTRACT

Staphylococcus aureus
is one of the major pathogens causing bovine mastitis, which results in huge economic losses in the dairy industry worldwide. Here, we report genome sequences of 17
S
.
aureus
strains, with three novel sequencing types (ST8495, ST8500, and ST8501) isolated from the milk of dairy cows with subclinical mastitis.
Draft genome sequence of a mosquito repellent
Bacillus licheniformis
strain Ba1 isolated from desert soil
Authors: Chouati Taha , Maski Soufiane , Melloul Marouane , Ajdig Mohammed , Ouchari Lahcen , Rached Bahia , El Fahime Elmostafa 
Published: November 2023

ABSTRACT

Microbial volatile organic compounds have been shown to affect a wide insect behavior. In this paper, we report the draft genome sequence of
Bacillus licheniformis
strain Ba1 previously isolated from desert soil in Morocco. The assembled and annotated draft genome contains 4,726 coding genes, 6 rRNAs and 97 tRNAs.