bluuebunny/crossref_metadata_2025_split huggingface dataset:
Using old and new approaches: determining physical properties of brown dwarfs with empirical relations and machine learning models
Authors: Feeser S Jean , Best William M J 
Published: March 2022

ABSTRACT
We investigate applications of machine learning models to directly infer physical properties of brown dwarfs from their photometry and spectra using The Cannon. We demonstrate that absolute magnitudes, spectral types, and spectral indices can be determined from low-resolution SpeX prism spectra of L and T dwarfs without trigonometric parallax measurements and with precisions competitive with commonly used methods. For T dwarfs with sufficiently precise spectra and photometry, bolometric luminosities and effective temperatures can be determined at precisions comparable to methods that use polynomial relations as a function of absolute magnitudes. We also provide new and updated polynomial relations for absolute magnitudes as a function of spectral types L0–T8 in 14 bands spanning Pan-STARRS rP1 to AllWISE W3, using a volume-limited sample of 256 brown dwarfs defined entirely by parallaxes. These include the first relations for brown dwarfs using Pan-STARRS1 photometry and the first for several infrared bands using a volume-limited sample. We find that our novel method with The Cannon can infer absolute magnitudes with equal or smaller uncertainties than the polynomial relations that depend on trigonometric parallax measurements.
Racial Differences in Patients Undergoing Anterior Cervical Discectomy and Fusion
Authors: Woodard Thaddeus K. , Cortese Brian D. , Gupta Sachin , Mohanty Sarthak , Casper David S. , Saifi Comron 
Published: March 2022

Study Design:
This was a retrospective chart review.

Objective:
The objective of this study was to examine disparities within patients undergoing anterior cervical discectomy and fusion (ACDF) at a multi-site tertiary referral center with specific focus on factors related to length of stay (LOS).

Summary of Background Data:
There are previously described racial disparities in spinal surgery outcomes and quality metrics.

Methods:
A total of 278 consecutive patients undergoing ACDF by 8 different surgeons over a 5-year period were identified retrospectively. Demographic data, including age at time of surgery, sex, smoking status, and self-identified race [White or African American (AA)], as well as surgical data and postoperative course were recorded. Preoperative health status was recorded, and comorbidities were scored by the Charlson Comorbidity Index. Univariable and multivariable linear regression models were employed to quantify the degree to which a patient’s LOS was related to their self-identified race, demographics, and perioperative clinical data.

Results:
Of the 278 patients who received an ACDF, 71.6% (199) self-identified as White and 28.4% (79) identified as AA. AA patients were more likely to have an ACDF due to myelopathy, while White patients were more likely to have an ACDF due to radiculopathy (P=0.001). AA patients had longer LOS by an average of half a day (P=0.001) and experienced a larger percentage of extended stays (P=0.002). AA patients experienced longer overall operation times on average (P=0.001) across all different levels of fusion. AA race was not an independent driver of LOS (β=0.186; P=0.246).

Conclusions:
As hypothesized, and consistent with previous literature on racial surgical disparities, AA race was associated with increased LOS, increased operative times, and increased indication of myelopathy in this study. Additional research is necessary to evaluate the underlying social determinants of health and other factors that may contribute to this study’s results.

Level of Evidence:
Level III.
Microscopic Anterior Cervical Discectomy and Fusion Versus Posterior Percutaneous Endoscopic Cervical Keyhole Foraminotomy for Single-level Unilateral Cervical Radiculopathy
Authors: Guo Linlin , Wang Jiajing , Zhao Zhen , Li Jing , Zhao Hongyang , Gao Yong , Chen Chao 
Published: March 2022

Study Design:
A systematic review and meta-analysis.

Objective:
The objective of this study was to compare the safety of microscopic anterior cervical discectomy and fusion (MI-ACDF) and posterior percutaneous endoscopic keyhole foraminotomy (PPEKF) in patients diagnosed with single-level unilateral cervical radiculopathy.

Summary of Background Data:
After conservative treatment, the symptoms will be relieved in about 90% of cervical radiculopathy patients. For the other one tenth of patients, surgical treatment is needed. The overall complication rate of MI-ACDF and PPEKF ranges from 0% to 25%, and the reoperation rate ranges from 0% to 20%.

Materials and Methods:
Electronic retrieval of studies from PubMed, Embase, and Cochrane Library was performed to identify comparative or single-arm studies on MI-ACDF and PPEKF. A total of 24 studies were included in our meta-analysis by screening according to the inclusion and exclusion criteria. After data extraction and quality assessment of the included studies, a meta-analysis was performed by using the R software. The pooled incidences of efficient rate, total complication rate, and reoperation rate were calculated.

Results:
A total of 24 studies with 1345 patients (MI-ACDF: 644, PPEKF: 701) were identified. There was no significantly statistical difference in pooled patient effective rate (MI-ACDF: 94.3% vs. PPEKF: 93.3%, P=0.625), total complication rate (MI-ACDF: 7.1% vs. PPEKF: 4.7%, P=0.198), and reoperation rate (MI-ACDF: 1.8% vs. PPEKF: 1.1%, P=0.312). However, the common complications of the 2 procedures were different. The most common complications of MI-ACDF were dysphagia and vertebral body sinking, whereas the most common complication of PPEKF was nerve root palsy.

Conclusions:
Both MI-ACDF and PPEKF can provide a relatively safe and reliable treatment for single-level unilateral cervical radiculopathy. The 2 techniques are not significantly different in terms of effective rate, total complication rate, and reoperation rate.
Early Plasma Nuclear DNA, Mitochondrial DNA, and Nucleosome Concentrations Are Associated With Acute Kidney Injury in Critically Ill Trauma Patients
Authors: Faust Hilary E. , Oniyide Oluwatosin , Wang Yiyue , Forker Caitlin M. , Dunn Thomas , Yang Wei , Lanken Paul N. , Sims Carrie A. , Yehya Nadir , Christie Jason D. , Meyer Nuala J. , Reilly John P. , Mangalmurti Nilam S. , Shashaty Michael G. S. 
Published: March 2022

OBJECTIVES:
Circulating nucleic acids, alone and in complex with histones as nucleosomes, have been proposed to link systemic inflammation and coagulation after trauma to acute kidney injury (AKI). We sought to determine the association of circulating nucleic acids measured at multiple time points after trauma with AKI risk.

DESIGN:
We conducted a prospective cohort study of trauma patients, collecting plasma on presentation and at 6, 12, 24, and 48 hours, defining AKI over the first 6 days by Kidney Disease Improving Global Outcomes serum creatinine and dialysis criteria. We determined kinetics of plasma mitochondrial DNA (mtDNA), nuclear DNA (nDNA), and nucleosome levels across time points and associations with AKI using multivariable linear mixed-effects models, adjusted for injury characteristics and blood transfusions. We evaluated the association of presentation nucleic acid damage-associated molecular patterns (DAMP) concentrations with subsequent AKI, adjusting for injury severity using multivariable logistic regression.

SETTING:
Academic level I trauma center.

PATIENTS:
Trauma patients (n = 55) requiring intensive care for greater than or equal to 24 hours after presentation.

INTERVENTIONS:
None.

MEASUREMENTS AND MAIN RESULTS:
AKI developed in 17 patients (31%), a median of 12.0 hours (interquartile range, 6.2–24.1 hr) after presentation. mtDNA demonstrated a time-varying association with AKI (p = 0.022, interaction with time point), with differences by AKI status not emerging until 24 hours (β = 0.97 [95% CI, 0.03–1.90] log copies/uL; p = 0.043). Patients who developed AKI had higher nDNA across all time points (overall β = 1.41 log copies/uL [0.86–1.95 log copies/uL]; p < 0.001), and presentation levels were significantly associated with subsequent AKI (odds ratio [OR], 2.55 [1.36–4.78] per log copy/uL; p = 0.003). Patients with AKI had higher nucleosome levels at presentation (β = 0.32 [0.00–0.63] arbitrary unit; p = 0.048), a difference that was more pronounced at 24 hours (β = 0.41 [0.06–0.76]; p = 0.021) and 48 hours (β = 0.71 [0.35–1.08]; p < 0.001) (p = 0.075, interaction with time point).

CONCLUSIONS:
Plasma nucleic acid DAMPs have distinct kinetics and associations with AKI in critically ill trauma patients. nDNA at presentation predicts subsequent AKI and may be amenable to targeted therapies in this population.
MYCOBACTERIUM ABSCESSUS SCLERAL BUCKLE INFECTION
Authors: Cai Sophie , Song Ailin , Borkar Durga S. 
Published: March 2022

Purpose:
To report the successful management of a rare case of Mycobacterium abscessus scleral buckle infection.

Methods:
Case report.

Results:
A 63-year-old woman with a history of sarcoid anterior uveitis and macula-off retinal detachment repaired by scleral buckle and pars plana vitrectomy presented with eye pain, redness, and purulent drainage in the left eye. Slit-lamp examination showed superonasal scleral buckle exposure, purulent conjunctival discharge, corneal edema, nongranulomatous keratic precipitates, and anterior chamber cell and flare. The patient underwent urgent scleral buckle removal. Intraoperatively, an area of scleral thinning without perforation underneath the exposed buckle was discovered and covered with a scleral patch graft, and an amniotic membrane graft was used to cover an area of bare sclera with significant conjunctival scarring and retraction. Cultures grew M. abscessus panresistant except to amikacin. After 6 weeks of fortified amikacin drops and a long taper of topical steroid therapy for persistent postoperative anterior uveitis, the patient's symptoms resolved.

Conclusion:

Mycobacterium is an emerging causative agent of scleral buckle infections. Our report provides insights about the management of such cases.
Local CCL18 and CCL21 expand lung fibrovascular niches and recruit lymphocytes, leading to tertiary lymphoid structure formation in prolonged COVID-19
Authors: Mothes Ronja , Pascual-Reguant Anna , Koehler Ralf , Liebeskind Juliane , Liebheit Alina , Bauherr Sandy , Dittmayer Carsten , Laue Michael , von Manitius Regina , Elezkurtaj Sefer , Durek Pawel , Heinrich Frederik , Heinz Gitta Anne , Guerra Gabriela Maria , Obermayer Benedikt , Meinhardt Jenny , Ihlow Jana , Radke Josefine , Heppner Frank L. , Enghard Philipp , Stockmann Helena , Aschman Tom , Schneider Julia , Corman Victor , Sander Leif Erik , Mashreghi Mir-Farzin , Conrad Thomas , Hocke Andreas , Niesner Raluca A. , Radbruch Helena , Hauser Anja E. 
Published: March 2022

AbstractPost-acute lung sequelae of COVID-19 are challenging many survivors across the world, yet the mechanisms behind are poorly understood. Our results delineate an inflammatory cascade of events occurring along disease progression within fibrovascular niches. It is initiated by endothelial dysfunction, followed by heme scavenging of CD163+ macrophages and production of CCL18. This chemokine synergizes with local CCL21 upregulation to influence the stromal composition favoring endothelial to mesenchymal transition. The local immune response is further modulated via recruitment of CCR7+ T cells into the expanding fibrovascular niche and imprinting an exhausted, T follicular helper–like phenotype in these cells. Eventually, this culminates in the formation of tertiary lymphoid structures, further perpetuating chronic inflammation. Thus, our work presents misdirected immune-stromal interaction mechanisms promoting a self-sustained and non-resolving local immune response that extends beyond active viral infection and leads to profound tissue repurposing and chronic inflammation.
High temperature increases centromere-mediated genome elimination frequency in Arabidopsis deficient in cenH3 or its assembly factor KNL2
Authors: Ahmadli Ulkar , Kalidass Manikandan , Khaitova Lucie Crhak , Fuchs Joerg , Cuacos Maria , Demidov Dmitri , Zuo Sheng , Pecinkova Jana , Mascher Martin , Ingouff Mathieu , Heckmann Stefan , Houben Andreas , Riha Karel , Lermontova Inna 
Published: March 2022

AbstractDouble haploid production is the most effective way of creating true-breeding lines in a single generation. In Arabidopsis, haploid induction via mutation of the centromere-specific histone H3 (cenH3) has been shown when outcrossed to wild-type. Here we report that a mutant of the cenH3 assembly factor KNL2 can be used as a haploid inducer. We elucidated that short temperature stress of the knl2 mutant increased the efficiency of haploid induction from 1 to 10%. Moreover, we have demonstrated that a point mutation in the CENPC-k motif of KNL2 is sufficient to generate haploid inducing lines, suggesting that haploid inducing lines in crops can be identified in a naturally occurring or chemically induced mutant population, avoiding the GMO approach at any stage. In addition, we have shown that the cenh3-4 mutant, which does not induce haploids under standard growth conditions, functions as a haploid inducer after exposure to short temperature stress.
Benchmarking computational methods for B-cell receptor reconstruction from single-cell RNA-seq data
Authors: Andreani Tommaso , Slot Linda M. , Gabillard Samuel , Struebing Carsten , Reimertz Claus , Veeranagouda Yaligara , Bakker Aleida M. , Olfati-Saber Reza , Toes Rene’ E. M. , Scherer Hans U. , Augé Franck , Šimaitė Deimantė 
Published: March 2022

ABSTRACTMultiple methods have recently been developed to reconstruct full-length B-cell receptors (BCRs) from single-cell RNA-seq (scRNA-seq) data. This need emerged from the expansion of scRNA-seq techniques, the increasing interest in antibody-based drug development and the importance of BCR repertoire changes in cancer and autoimmune disease progression. However, a comprehensive assessment of performance-influencing factors like the sequencing depth, read length or the number of somatic hypermutations (SHMs) as well as guidance regarding the choice of methodology are still lacking. In this work, we evaluated the ability of six available methods to reconstruct full-length BCRs using one simulated and three experimental SMART-seq datasets. In addition, we validated that the BCRs assembled in silico recognize their intended targets when expressed as monoclonal antibodies. We observed that methods like BALDR, BASIC and BRACER showed the best overall performance across the tested datasets and conditions whereas only BASIC demonstrated acceptable results on very short read libraries. Furthermore, the de novo assembly-based methods BRACER and BALDR were the most accurate in reconstructing BCRs harboring different degrees of SHMs in the variable domain, while TRUST4, MiXCR and BASIC were the fastest. Finally, we propose guidelines to select the best method based on the given data characteristics.
m6A RNA methylation impairs gene expression variability and reproductive thermotolerance inArabidopsis
Authors: Wang Ling , Zhuang Haiyan , Fan Wenwen , Zhang Xia , Dong Haihong , Yang Hongxing , Cho Jungnam 
Published: March 2022

AbstractPlants are more susceptible to high temperature stress during reproductive development, which can cause drastic yield loss of fruit and seed crops. Unfortunately, the underlying mechanism remains largely unknown. Here we suggest that m6A RNA methylation level increases in the reproductive tissues ofArabidopsisand negatively regulates gene expression variability. It has been suggested that stochasticity of gene expression can be advantageous to fitness of living organisms under environmental challenges. Indeed, reduced gene expression variability in flowers was associated with compromised transcriptional activation of heat-responsive genes. Importantly, disruption of an RNA demethylaseAtALKBH10Bled to lower gene expression variability, hypo-responsiveness of heat-activated genes, and strong reduction of plant fertility. Overall, our work proposes a novel mechanism that m6A RNA modification mediates the bet-hedging strategy of plants challenged by heat stress.
A Cellular Taxonomy of the Adult Human Spinal Cord
Authors: Yadav Archana , Matson Kaya J.E. , Li Li , Hua Isabelle , Petrescu Joana , Kang Kristy , Alkaslasi Mor R. , Lee Dylan I. , Hasan Saadia , Galuta Ahmad , Dedek Annemarie , Ameri Sara , Parnell Jessica , Alshardan Mohammad M. , Qumqumji Feras Abbas , Alhamad Saud M. , Wang Alick Pingbei , Poulen Gaetan , Lonjon Nicolas , Vachiery-Lahaye Florence , Gaur Pallavi , Nalls Mike A. , Qi Yue A. , Ward Michael E. , Hildebrand Michael E. , Mery Pierre-Francois , Bourinet Emmanuel , Bauchet Luc , Tsai Eve C. , Phatnani Hemali , Le Pichon Claire E. , Menon Vilas , Levine Ariel J. 
Published: March 2022

AbstractThe mammalian spinal cord functions as a community of glial and neuronal cell types to accomplish sensory processing, autonomic control, and movement; conversely, the dysfunction of these cell types following spinal cord injury or disease states can lead to chronic pain, paralysis, and death. While we have made great strides in understanding spinal cellular diversity in animal models, it is crucial to characterize human biology directly to uncover specialized features of basic function and to illuminate human pathology. Here, we present a cellular taxonomy of the adult human spinal cord using single nucleus RNA-sequencing with spatial transcriptomics and antibody validation. We observed 29 glial clusters, including rare cell types such as ependymal cells, and 35 neuronal clusters, which we found are organized principally by anatomical location. To demonstrate the potential of this resource for understanding human disease, we analyzed the transcriptome of spinal motoneurons that are prone to degeneration in amyotrophic lateral sclerosis (ALS) and other diseases. We found that, compared with all other spinal neurons, human motoneurons are defined by genes related to cell size, cytoskeletal structure, and ALS, thereby supporting a model of a specialized motoneuron molecular repertoire that underlies their selective vulnerability to disease. We include a publicly available browsable web resource with this work, in the hope that it will catalyze future discoveries about human spinal cord biology.
Transcriptome analysis reveals robust transcriptional reprogramming during early stages of Cicer-Ascochyta interaction
Authors: Singh Ritu , Dwivedi Aditi , Singh Yeshveer , Kumar Kamal , Ranjan Aashish , Verma Praveen Kumar 
Published: March 2022

ABSTRACTAscochyta blight (AB) caused by a filamentous fungus Ascochyta rabiei is a major threat to global chickpea production. The mechanisms underlying chickpea response to A. rabiei remain elusive. Here, we investigated the comparative transcriptional dynamics of AB-resistant and susceptible chickpea genotypes upon A. rabiei infection to understand the early host defence response. Our findings revealed that AB-resistant plants underwent rapid and extensive transcriptional reprogramming compared to susceptible host. At early stage (24-hpi), mainly cell wall remodeling and secondary metabolite pathways were highly activated, while DEGs related with signaling components viz. protein kinases, transcription factors, and hormonal pathways show remarkable upsurge at 72-hpi, especially in resistant genotype. Notably, our data suggests imperative role of JA, ET, and ABA signaling in providing immunity against A. rabiei. Furthermore, gene co-expression networks and modules corroborated the importance of cell wall remodeling, signal transduction and phytohormone pathways. The hub genes such as MYB14, PRE6 and MADS-SOC1 discovered in these modules might be the master regulators governing chickpea immunity. Overall, we not only provide novel insights for comprehensive understanding of immune signaling components mediating AB resistance/susceptibility at early Cicer-Ascochyta interactions, but also offer a valuable resource for developing AB-resistant chickpea.HighlightsComparative transcriptomic and co-expression analysis of AB-resistant and susceptible chickpea genotypes reveals high-amplitude transcriptional dynamics in resistant plants, and also identifies TFs, PKs and phytohormone-crosstalk as core regulators for AB-resistance.
Knockout of TSPO delays and reduces amyloid, Tau, astrocytosis and behavioral dysfunctions in Alzheimer’s disease
Authors: Ceyzériat Kelly , Meyer Léa , Bouteldja Farha , Tsartsalis Stergios , Amossé Quentin , Middleton Ryan J. , Liu Guo-Jun , Banati Richard B. , Zilli Thomas , Garibotto Valentina , Millet Philippe , Tournier Benjamin B. 
Published: March 2022

AbstractThe 18kDa translocator protein (TSPO) is up-regulated in glial cells in neurodegenerative diseases. In Alzheimer’s disease (AD) animal models, TSPO is first overexpressed in astrocytes and then in microglia. However, the precise role of TSPO in the onset and progression of pathology and symptoms characteristic of the disease remains unknown. Here, we report that in the absence of TSPO in 3xTgAD mice the expected disease onset is significantly delayed and a reduction is seen in the hippocampal load of poorly and highly aggregated forms of Tau (−44% and −82%, respectively) and Aβ42 (−25% and −95%, respectively), at 9 months of age. In addition, the astrocyte reactivity was decreased in 3xTgAD.TSPO−/− mice with a reduction in the morphologic complexity and the size of astrocytes in the dorso-dorsal hippocampus and the hilus. Functionally, the absence of TSPO ameliorated the cognitive consequences of adeno-associated virus-induced Tau over-expression in the hippocampus. This suggests that TSPO plays an important role in the active disease progression of AD. TSPO-inhibiting drugs thus merit further exploration as to their potential to reduce the rate of neurodegenerative disease progression.
Differences in homologous recombination and maintenance of heteropolyploidy between Haloferax volcanii and Haloferax mediterranei
Authors: Dattani Ambika , Sharon Itai , Shtifman-Segal Ella , Robinzon Shachar , Gophna Uri , Allers Thorsten , Altman Neta 
Published: March 2022

AbstractPolyploidy, the phenomenon of having more than one copy of the genome in an organism, is common among haloarchaea. While providing short-term benefits for DNA repair, polyploidy is generally regarded as an ‘evolutionary trap’ that by the notion of the Muller’s ratchet will inevitably conclude in the species’ decline or even extinction due to a gradual reduction in fitness. In most reported cases of polyploidy in archaea, the genetic state of the organism is considered as homoploidy i.e. all copies of the genome are identical. Here we demonstrate that while this is indeed the prevalent genetic status in the halophilic archaeon H. volcanii, its close relative H. mediterranei maintains a prolonged heteroploidy state in a non-selective environment once a second allele is introduced. Moreover, a strong genetic linkage was observed between two distant loci in H. mediterranei indicating a low rate of homologous recombination while almost no such linkage was shown in H. volcanii indicating a high rate of recombination in the latter species.We suggest that H. volcanii escapes Muller’s ratchet by means of an effective chromosome-equalizing gene-conversion mechanism facilitated by highly active homologous recombination, whereas H. mediterranei must elude the ratchet via a different, yet to be elucidated mechanism.