bluuebunny/crossref_metadata_2025_split huggingface dataset:
Complete Genome Sequence of Bacillus velezensis TH-1, a Candidate Biocontrol Bacterium from China
Authors: He Pengjie , Tang Xiaodi , Wei Shenghua , An Jiangyong , Cui Wenyan 
Published: February 2023

Bacillus velezensis TH-1 is a plant growth–promoting rhizobacteria with biocontrol potential that was isolated from the rhizosphere of Sophora tonkinensis Radix . Our previous results showed that strain TH-1 demonstrated effective biocontrol activity against root rot of Sophora tonkinensis Radix and bacterial wilt of ginger. Currently, only a few whole-genome sequences of biocontrol strains isolated from the rhizosphere of medicinal plants are available. We report, here, the complete genome sequence of B. velezensis TH-1. The size of TH-1 genome is 3,929,846 bp that consists of 3,900 genes with a total GC content of 46.48%. The strain TH-1 genome has 3,661 coding genes, 86 transfer RNAs, 27 ribosomal RNAs, and 16 small RNAs. Moreover, we identified nine gene clusters coding for the biosynthesis of antimicrobial compounds. The genomic information of TH-1 will provide resources for the study of biological control mechanisms and plant-microbe interactions. [Formula: see text] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .
Congenital Synostosis of the Knee: Long-term Outcomes of Limb Reconstruction Surgery
Authors: Belthur Mohan V. , Huser Aaron J. , Nahm Nickolas J. , McClure Philip K. , Burghardt Rolf D. , Segev E. , Wientroub Shlomo , Paley Dror , Herzenberg John E. 
Published: February 2023

Background:
Congenital synostosis of the knee is a rare condition with limited data on treatment options and outcomes. This study reports clinical findings, treatment approach, and surgical/clinical outcomes for congenital synostosis of the knee.

Methods:
An institutional review board-approved retrospective review of patients with congenital synostosis of the knee presenting to 2 institutions between 1997 and 2021 was performed.

Results:
Eight patients (13 knees) with a median follow-up of 11.3 years (3.3 to 17 y) were included. Seven patients had associated syndromes. Patients presented with an average knee flexion deformity of 100° (range 60 to 130°) and delayed walking ability. Seven patients had associated upper extremity hypoplasia/phocomelia. The average age at the index surgery was 4.3 years (range 1.2 to 9.2 y). Synostosis resection with gradual deformity correction was performed in most patients. An attempt was made at a mobile knee in some patients, but all went on to knee fusion. Mean flexion deformity at final follow-up was 11.6° (range: 0 to 40°) and 5 limbs were fused in full extension. Mean limb length discrepancy at final follow-up was 6.8 cm (range: 0 to 8 cm). All patients maintained their improved ambulation status at final follow-up. Twenty-two complications were identified.

Conclusions:
Reliable correction of the deformity associated with congenital knee synostosis was achieved at a median follow-up of 11 years. Importantly, all patients maintained their improved ambulation at final follow-up. This is the largest study on patients with congenital knee synostosis and outlines a reconstructive approach to improve ambulatory status.

Level of Evidence:
Level IV
Scoliosis and Kyphosis Prevalence in Turner Syndrome: A Retrospective Review at a Pediatric Tertiary Care Medical Center
Authors: Marx Jeremy S. , Pagadala Manasa , Carney John , Gerlach Erik , Swiatek Peter , Zabinsky Jennifer A. , Sarwark John , Brickman Wendy J. , Habiby Reema L. 
Published: February 2023

Background:
The prevalence of major coronal and sagittal spinal curves (scoliosis and kyphosis) in Turner syndrome (TS) is not well established due to limited reporting. The relationship between growth hormone (GH) therapy and its effect on TS spinal curve incidence is also not well established.

Methods:
A retrospective chart review of 306 TS patients from 2007 to 2021 evaluated major coronal and sagittal spinal curves, progression of the curve, and treatment with GH. Statistical significance (defined as P <0.05) between curvature rates and curve progression was compared between GH-treated patients and non–GH-treated patients using a χ2 or Fisher exact test when appropriate.

Results:
Thirty-seven of 306 (12%) TS patients had a radiographically relevant spinal deformity. Twenty-seven of 37 (73%) had mild; 4 of 37 (11%) had moderate, and 6 of 37 (16%) had severe curves. Of those with severe, 4 underwent spinal fusion, 1 was treated with bracing, and 1 was braced before a cardiovascular-related death. Regarding GH use among TS patients, 190 of 306 (62%) used GH versus 116 of 306 (38%) who did not. Of those with a spinal curve, 24 of 37 (65%) used GH compared with 13 of 37 (35%) who did not. On univariate analysis, GH therapy was not a risk factor for the diagnosis of a major spinal curve, a more severe degree of the curve at the time of diagnosis, or spinal curve progression (P >0.05 for all).

Conclusions:
This is the largest single institution retrospective review of a TS cohort known to the authors assessing spinal curve prevalence and relation to GH treatment and demonstrates a TS spinal curve rate of 12% (37/306). Four of six (11%) TS patients with a severe curve underwent corrective spine fusion. There was no relationship between the use of GH and the presence of a spinal curve or curve progression. Further study is warranted to determine risk factors for curve progression.

Level of Evidence:
Level III.

Clinical Relevance:
This retrospective case series serves to review and address the prevalence of spinal deformity in TS patients and whether GH impacts worsening deformity.
Applying principal component pursuit to investigate the association between source-specific fine particulate matter and myocardial infarction hospitalizations in New York City
Authors: Tao Rachel H. , Chillrud Lawrence G. , Nunez Yanelli , Rowland Sebastian T. , Boehme Amelia K. , Yan Jingkai , Goldsmith Jeff , Wright John , Kioumourtzoglou Marianthi-Anna 
Published: February 2023

Background:
The association between fine particulate matter (PM2.5) and cardiovascular outcomes is well established. To evaluate whether source-specific PM2.5 is differentially associated with cardiovascular disease in New York City (NYC), we identified PM2.5 sources and examined the association between source-specific PM2.5 exposure and risk of hospitalization for myocardial infarction (MI).

Methods:
We adapted principal component pursuit (PCP), a dimensionality-reduction technique previously used in computer vision, as a novel pattern recognition method for environmental mixtures to apportion speciated PM2.5 to its sources. We used data from the NY Department of Health Statewide Planning and Research Cooperative System of daily city-wide counts of MI admissions (2007–2015). We examined associations between same-day, lag 1, and lag 2 source-specific PM2.5 exposure and MI admissions in a time-series analysis, using a quasi-Poisson regression model adjusting for potential confounders.

Results:
We identified four sources of PM2.5 pollution: crustal, salt, traffic, and regional and detected three single-species factors: cadmium, chromium, and barium. In adjusted models, we observed a 0.40% (95% confidence interval [CI]: –0.21, 1.01%) increase in MI admission rates per 1 μg/m3 increase in traffic PM2.5, a 0.44% (95% CI: –0.04, 0.93%) increase per 1 μg/m3 increase in crustal PM2.5, and a 1.34% (95% CI: –0.46, 3.17%) increase per 1 μg/m3 increase in chromium-related PM2.5, on average.

Conclusions:
In our NYC study, we identified traffic, crustal dust, and chromium PM2.5 as potentially relevant sources for cardiovascular disease. We also demonstrated the potential utility of PCP as a pattern recognition method for environmental mixtures.
Are serum uric acid levels predictors of cardiovascular risk? An update
Authors: Georgoulis Michael , Mikhailidis Dimitri P. , Panagiotakos Demosthenes B. 
Published: February 2023

Purpose of review
The aim of this review was to update the evidence regarding the link between serum uric acid and cardiovascular risk, as well as the role of nutrition in the prevention and management of hyperuricaemia.

Recent findings
The review focuses on recent epidemiological evidence concerning the role of elevated serum uric acid levels in cardiovascular risk prediction. The dietary prevention and management of hyperuricaemia is also discussed with an emphasis on the adoption of prudent dietary patterns.

Summary
There is evidence supporting that elevated serum uric acid levels are positively associated with cardiovascular disease risk and might represent a useful additional marker for risk stratification. The association of serum uric acid with all-cause and cardiovascular mortality seems to be U-shaped, suggesting that both very low and very high serum uric acid levels might be detrimental for survival, the former being mediated by malnutrition. Apart from medication, the dietary management of hyperuricaemia should focus on the adoption of a prudent dietary pattern, such as the Mediterranean diet, which can both prevent gout and mitigate cardiometabolic risk.
Magnetic Resonance Imaging Virtual Biopsy of Common Solid Renal Masses—A Pictorial Review
Authors: Kumar Sindhu , Virarkar Mayur , Vulasala Sai Swarupa R. , Daoud Taher , Ozdemir Savas , Wieseler Carissa , Vincety-Latorre Fiorella , Gopireddy Dheeraj R. , Bhosale Priya , Lall Chandana 
Published: February 2023

Abstract
The expanded application of radiologic imaging resulted in an increased incidence of renal masses in the recent decade. Clinically, it is difficult to determine the malignant potential of the renal masses, thus resulting in complex management. Image-guided biopsies are the ongoing standard of care to identify molecular variance but are limited by tumor accessibility and heterogeneity. With the evolving importance of individualized cancer therapies, radiomics has displayed promising results in the identification of tumoral mutation status on routine imaging. This article discusses how magnetic resonance imaging features can guide a radiologist toward identifying renal mass characteristics.
The Outcome of Transplanting Kidneys From Very Small Pediatric Deceased Donors
Authors: Zhang Qiang , Su Xiaojun , Liu Longshan , Huang Mingchuan , Wu Wenrui , Zhang Huanxi , Wu Chenglin , Fu Qian , Gao Pengfei , Ling Liuting , Chen Wenting , Xu Bowen , Liao Yuan , Li Jun , Wang Changxi 
Published: February 2023

Background.Kidneys from very small pediatric donors (VSPDs, aged <2 y) are underutilized. Concerns regarding potentially inferior outcomes hinder the use in pediatric recipients.Methods.All pediatric kidney-only transplants from <18-year-old donors between January 2012 and May 2021 in our center were included in this study. Outcomes were compared between VSPD and normal pediatric donor (NPD, aged 2–18 y) groups, and 3-y death-censored graft survival was assessed by the multivariable Cox proportional hazard model.Results.Of all 252 enrolled patients, 149 (59.1%) received kidneys from NPDs and 103 (40.9%) from VSPDs. The 3-y graft survival rates of the NPD and VSPD groups were 91.2% and 88.6%, respectively (P= 0.385). The adjusted hazard ratio of 3-y graft loss was 1.2 (95% confidence interval, 0.6-2.5;P= 0.659) for the VSPD group compared with the NPD group. There was no significant difference in estimated glomerular filtration rate at 3 y posttransplant observed between NPD and VSPD groups (86.9 ± 26.8 versus 87 ± 27.9 mL/min/1.73 m2;P= 0.991). Patients (n = 12, 4.8%) who received kidneys from donors <5 kg contributed 5 (5/39, 12.8%) with delayed graft function and the sole primary nonfunction in our cohort.Conclusions.Although attention to preventing complications is necessary, especially for kidneys from donors <5 kg, kidneys from VSPDs did not appear to impart added risk for 3-y graft loss and renal function.
Abyssibius alkaniclasticus gen. nov., sp. nov., a novel member of the family Rhodobacteraceae, isolated from the Mariana Trench
Authors: Wei Ting-Ting , Fan Xi-Bei , Quan Zhe-Xue 
Published: February 2023

A Gram-stain-negative bacterium with rod-shaped or irregular cells approximately 0.5–0.9×2.0–3.8 µm in size, designated as 960558T, was isolated from sediment sampled in the Mariana Trench. Strain 960558T grows at 4–37 °C (optimum, 28 °C), pH 6–7 (optimum, pH 7) and in the presence of 1–5 % (w/v) NaCl (optimum, 3 %). Strain 960558T utilizes tetradecane or hexadecane as a sole carbon and energy source, respectively. Phylogenetic trees based on 16S rRNA gene sequences and phylogenomic reconstruction revealed a close phylogenetic relationship between strain 960558T and members of the family

Rhodobacteraceae

by forming a separate branch within the type species of closely related genera. The validly published species that is most closely related to strain 960558T is

Planktotalea lamellibrachiae

JAM 119T, which has the highest 16S rRNA gene sequence similarity (93.47 %). Ubiquinone 10 is the predominant ubiquinone, while C16 : 0, 11-methyl C18 : 1
ω7c and C18 : 1
ω7c and/or C18 : 1
ω6c are the predominant fatty acids (>10 %). Additionally, phosphatidylglycerol, glycolipids, diphosphatidylglycerol, unidentified polar lipids and unidentified aminolipids are the major polar lipids. The DNA G+C content of strain 960558T is 61 %. Average nucleotide identity and digital DNA–DNA hybridization results of strain 960558T with other type strains are <70.2 and 22.1 %, respectively. Based on its phylogenetic, chemotaxonomic and other phenotypic properties, strain 960558T is considered to represent a novel genus and species within the family

Rhodobacteraceae

, for which the name Abyssibius alkaniclasticus gen. nov., sp. nov. is proposed. The type strain of Abyssibius alkaniclasticus is 960558T (=KCTC 82619T=MCCC 1K04727T).
Corticolimbic connectivity mediates the relationship between pubertal timing and mental health problems
Authors: Vijayakumar Nandita , Whittle Sarah , Silk Timothy J. 
Published: February 2023

AbstractBackgroundUndergoing puberty ahead of peers (“earlier pubertal timing”) is an important risk factor for mental health problems during early adolescence. The current study examined pathways between pubertal timing and mental health via connectivity of neural systems implicated in emotional reactivity and regulation (specifically corticolimbic connections) in 9- to 14-year-olds.MethodResearch questions were examined in the Adolescent Brain Cognitive Development (ABCD) Study, a large population representative sample in the United States. Linear mixed models examined associations between pubertal timing and resting-state corticolimbic connectivity. Significant connections were examined as potential mediators of the relationship between pubertal timing and mental health (withdrawn depressed and rule-breaking delinquency) problems. Exploratory analyses interrogated whether the family environment moderated neural risk patterns in those undergoing puberty earlier than their peers.ResultsEarlier pubertal timing was related to decreased connectivity between limbic structures (bilateral amygdala and right hippocampus) and the cingulo-opercular network (CON), as well as between the left hippocampus and ventral attention network (VAN). Corticolimbic connections also mediated the relationship between earlier pubertal timing and increased withdrawn depressed problems (but not rule-breaking delinquency). Finally, parental acceptance buffered against limbic-CON connectivity patterns that were implicated in withdrawn depressed problems in those undergoing puberty earlier than their peers.ConclusionFindings highlight the role of decreased corticolimbic connectivity in mediating pathways between earlier pubertal timing and withdrawn depressed problems, and we present preliminary evidence that the family environment may buffer against these neural risk patterns during early adolescence.
Distinctivein vitrophenotypes in iPSC-derived neurons from patients with gain- and loss-of-functionSCN2Adevelopmental and epileptic encephalopathy
Authors: Mao Miaomiao , Mattei Cristiana , Rollo Ben , Byars Sean , Cuddy Claire , Berecki Geza , Heighway Jacqueline , Pachernegg Svenja , Menheniott Trevelyan , Apted Danielle , Jia Linghan , Dalby Kelley , Nemiroff Alex , Mullen Saul , Reid Christopher A. , Maljevic Snezana , Petrou Steven 
Published: February 2023

AbstractSCN2Aencodes NaV1.2, an excitatory neuron voltage-gated sodium channel and major monogenic cause of neurodevelopmental disorders, including developmental and epileptic encephalopathies (DEE) and autism. Clinical presentation and pharmocosensitivity vary with nature ofSCN2Avariant dysfunction with gain-of-function (GoF) cases presenting with pre- or peri-natal seizures and loss-of-function (LoF) patients typically having infantile spasms after 6 months of age. Here, we established and assessed patient induced pluripotent stem cell (iPSC) - derived neuronal models for two recurrentSCN2ADEE variants with GoF R1882Q and LoF R853Q associated with early- and late-onset DEE, respectively.Patient-derived iPSC lines were differentiated using a Neurogenin-2 overexpression yielding populations of cortical-like glutamatergic neurons. Electrophysiological and transcriptomic profiles were assessed after 2-4 weeks in culture. Increased neuronal activity at both cellular and network level was observed for R1882Q iPSC-derived neurons at three weeks of differentiation. In contrast, R853Q neurons showed only subtle changes in excitability after four weeksin vitro. In alignment with the reported efficacy in some GoFSCN2Apatients, phenytoin (sodium channel blocker) reduced excitability of neurons to the control levels in R1882Q neuronal cultures. Transcriptomic alterations in neurons were detected for each variant and convergent pathways pointed at the shared mechanisms underlyingSCN2ADEE.
Taxonomic and diet-based functional structure of carabid communities varies seasonally in cultivated fields
Authors: Gaël Caro , Ronan Marrec , Cyril Auguste , Aude Barbottin 
Published: February 2023

AbstractAgricultural intensification has altered the provision of natural bioregulation. We assessed the effects of five different crops under non-inversion tillage on the temporal dynamics of carabid assemblages. We evaluated how the taxonomic diversity, the composition, and the diet-based functional structure of communities varied over the spring period.Carabid assemblages were monitored over 4 years (from 2009 to 2012), in a total of 67 fields (each field followed one year) cropped with either winter oilseed rape, winter wheat, sugar beet, spring barley, or spring pea. We assigned a relative diet profile to each species accounting for more than 0.5 % of the total mean abundance-activity: granivorous, phytophagous, and zoophagous.The seasonal changes in species richness, abundance-activity, and evenness had the same dynamic in all crops. Despite differences in species identities between crops, the zoophagous and phytophagous diet profiles showed similar temporal dynamics in all crop types, suggesting a high functional equivalence among species present in cultivated fields. Zoophagous species were progressively replaced by primarily phytophagous species in all crops, while the increase in granivorous species was only observed in oilseed rape.Our results suggest that potential bioregulation do not significantly differ among crop types but vary along the spring season.HighlightsWe monitored carabid communities in five crop types under non-inversion tillageWe observed similar seasonal increases in carabid abundance-activity and species richness in all crops during the spring periodWe observed similar trends in temporal changes in carnivorous and phytophagous diet profiles in all cropsWith seasonal changes, zoophagous species are progressively replaced by more phytophagous speciesCrop type is not the main factor driving temporal changes in diet-based structure of carabid assemblages
Shoot maturation strengthens FLS2-mediated resistance toPseudomonas syringae
Authors: Hu Lanxi , Kvitko Brian , Yang Li 
Published: February 2023

AbstractA temporal-spatial regulation of immunity components is essential for properly activating plant defense response. Flagellin-sensing 2 (FLS2) is a surface-localized receptor that recognizes bacterial flagellin. The immune function of FLS2 is compromised in early stages of shoot development. However, the underlying mechanism for the age-dependent FLS2 signaling is not clear. Here, we show that the reduced basal immunity of juvenile leaves againstPseudomonas syringaepv. tomato DC3000 is independent of FLS2. The flg22-induced marker gene expression and ROS activation were comparable in juvenile and adult stage, but callose deposition was more evident in the adult stage than that of juvenile stage. We further demonstrated that microRNA156, a master regulator of plant aging, suppressed callose deposition in juvenile leaves in response to flg22 but not the expression ofFLS2andFRK1 (Flg22-induced receptor-like kinase 1). Altogether, we revealed an intrinsic mechanism that regulates the amplitude of FLS2-mediated resistance during aging.
Inositol Pyrophosphate Dynamics Reveals Control of the Yeast Phosphate Starvation Program Through 1,5-IP8and the SPX Domain of Pho81
Authors: Chabert Valentin , Kim Geun-Don , Qiu Danye , Liu Guizhen , Mayer Lydie Michaillat , Muhammed Jamsheer K. , Jessen Henning Jacob , Mayer Andreas 
Published: February 2023

AbstractEukaryotic cells control inorganic phosphate to balance its role as essential macronutrient with its negative bioenergetic impact on reactions liberating phosphate. Phosphate homeostasis depends on the conserved INPHORS signaling pathway that utilizes inositol pyrophosphates (IPPs) and SPX receptor domains. Since cells synthesize various IPPs and SPX domains bind them promiscuously, it is unclear whether a specific IPP regulates SPX domains in vivo, or whether multiple IPPs act as a pool. In contrast to previous models, which postulated that phosphate starvation is signaled by increased production of the IPP 1-IP7, we now show that the levels of all detectable IPPs of yeast, 1-IP7, 5-IP7and 1,5-IP8, strongly decline upon phosphate starvation. Among these, specifically the decline of 1,5-IP8triggers the transcriptional phosphate starvation response, the PHO pathway. 1,5-IP8inactivates the cyclin-dependent kinase inhibitor Pho81 through its SPX domain. This stimulates the cyclin-dependent kinase Pho85-Pho80 to phosphorylate the transcription factor Pho4 and repress the PHO pathway. Combining our results with observations from other systems we propose a unified model where 1,5-IP8signals cytosolic phosphate abundance to SPX proteins in fungi, plants, and mammals. Its absence triggers starvation responses.Significance statementCytosolic Piis of prime importance for cellular bioenergetics because Piinfluences free energy of nucleotide hydrolysis and the metabolite fluxes through glycolysis and oxidative phosphorylation. Eukaryotic cells use the INPHORS pathway to signal Pivia SPX domains and their ligands, inositol pyrophosphates (IP7, IP8), which control Pihomeostasis through a network of target proteins that import, export, store or detoxify Pi. Studies with different systems failed to yield a coherent model on this regulation.We performed the first time-resolved profiling of the full isomer spectrum of inositol pyrophosphates in yeast and dissected the isomer that is relevant to intracellular Pisignaling. Our results can be combined with existing observations from plants, mammals, and other fungi to support a unified model of Pisignaling across all eukaryotic kingdoms, which is in accord with the fundamental importance of Pimanagement for metabolism.