bluuebunny/crossref_metadata_2025_split huggingface dataset:
Management of Macrocystic Lymphatic Malformation in the Cervicofacial Region
Authors: Han Tao , Chen Haini , Cui Jie , Shen Weimin 
Published: February 2022

Purpose
The purpose of our study was to evaluate the efficacy and safety of ultrasound-guided iodine tincture cauterization combined with postoperative intralesional negative pressure in the management of cervicofacial cystic lymphatic malformation (cLM).

Method
From January 2019 to July 2021, indocyanine green lymphography was performed preoperatively to confirm the lymph inflow, and this treatment was administered in 71 patients with cervicofacial cLM in our center. All cases were evaluated by curative effects, treatment frequency, and adverse events. The duration of posttreatment follow-up was from 12 to 14 months.

Results
Indocyanine green lymphography indicated at least one lymphatic inflow in each cLM lesion. Excellent resolution was observed in 87.3% of cases, and good improvement of the treated cLM occurred in 9.9% of cases, and 2 cases with fair outcomes required subsequent treatment. It is noteworthy that no case was treated more than 3 times. Some minor adverse effects, including localized itch and scar, were managed by symptomatic treatment.

Conclusions
Because of satisfactory outcomes and low treatment frequency, ultrasound-guided iodine tincture cauterization combined with intralesional negative pressure represents an efficacious, safe, and feasible method for the management of macro-cLM in the cervicofacial region.
Deciphering the contributions of neuroinflammation to neurodegeneration: lessons from antibody-mediated encephalitis and coronavirus disease 2019
Authors: Shir Dror , Day Gregory S. 
Published: February 2022

Purpose of reviewDoes neuroinflammation promote neurodegeneration? Does neurodegeneration promote neuroinflammation? Or, is the answer to both questions,yes? These questions have proven challenging to answer in patients with typical age-related neurodegenerative diseases in whom the onset of neuroinflammation and neurodegeneration are largely unknown. Patients recovering from diseases associated with abrupt-onset neuroinflammation, including rare forms of antibody-mediated encephalitis (AME) and common complications of novel coronavirus disease 2019 (COVID-19), provide a unique opportunity to untangle the relationship between neuroinflammation and neurodegeneration. This review explores the lessons learned from patients with AME and COVID-19.Recent findingsPersistent cognitive impairment is increasingly recognized in patients recovering from AME or COVID-19, yet the drivers of impairment remain largely unknown. Clinical observations, neuroimaging and biofluid biomarkers, and pathological studies imply a link between the severity of acute neuroinflammation, subsequent neurodegeneration, and disease-associated morbidity.SummaryData from patients with AME and COVID-19 inform key hypotheses that may be evaluated through future studies incorporating longitudinal biomarkers of neuroinflammation and neurodegeneration in larger numbers of recovering patients. The results of these studies may inform the contributors to cognitive impairment in patients with AME and COVID-19, with potential diagnostic and therapeutic applications in patients with age-related neurodegenerative diseases.
Sneathiella sedimenti sp. nov., isolated from marine sediment
Authors: Lee Yunjeong , Weerawongwiwat Veeraya , Kim Jong-Hwa , Yoon Jung-Hoon , Suh Min Kuk , Kim Han Sol , Lee Jung-Sook , Sukhoom Ampaitip , Kim Wonyong 
Published: February 2022

A novel bacterium, designated CAU 1612T, was isolated from coastal sediment sampled in the Republic of Korea. Cells of the strain were Gram-stain-negative, rod-shaped and motile. Optimum growth occurred at 30 °C, at pH 7.0 and with 1.0 % (w/v) NaCl. Based on 16S rRNA gene sequences, phylogenetic analysis revealed that strain CAU 1612T belonged to the genus

Sneathiella

and showed highest similarity to ‘Sneathiella litorea’ JCM 33810T (98.5 %), followed by

Sneathiella chungangensis

KCTC 32476T (97.7 %),

Sneathiella aquimaris

KCTC 12842T (96.0 %),

Sneathiella chinensis

LMG 23452T (95.5 %),

Sneathiella limimaris

KCTC 52846T (95.5 %) and

Sneathiella glossodoripedis

KCTC 12842T (95.4 %). The average nucleotide identity and digital DNA–DNA hybridization values of strain CAU 1612T were estimated to be 68.5–81.7 % and ≤23.7 %, respectively, to members of the genus

Sneathiella

. The DNA G+C content was 54.1 mol%. The major cellular fatty acids (>10 %) were C16:0, C19 : 0 cyclo ω8c and summed feature 8 (C18 : 1
ω7c and/or C18 : 1
ω6c). The major menaquinone was Q-10 and the predominant polar lipids were phosphatidylmethylethanolamine, phosphatidylethanolamine and phosphatidylglycerol. On the basis of taxonomic evidence, strain CAU 1612T represents a novel species, for which the name Sneathiella sedimenti sp. nov. is proposed. The type strain is CAU 1612T (=KCTC 82427T=MCCC 1K06082T).
Efficacy and Safety of a Booster Regimen of Ad26.COV2.S Vaccine against Covid-19
Authors: Hardt Karin , Vandebosch An , Sadoff Jerry , Gars Mathieu Le , Truyers Carla , Lowson David , Van Dromme Ilse , Vingerhoets Johan , Kamphuis Tobias , Scheper Gert , Ruiz-Guiñazú Javier , Faust Saul N. , Spinner Christoph D. , Schuitemaker Hanneke , Van Hoof Johan , Douoguih Macaya , Struyf Frank ,   the ENSEMBLE2 Study Group
Published: February 2022

ABSTRACTBackgroundDespite the availability of effective vaccines against coronavirus disease 2019 (Covid-19), the emergence of variant strains and breakthrough infections pose a challenging new reality. Booster vaccinations are needed to maintain vaccine-induced protection.MethodsENSEMBLE2 is an ongoing, randomized, double-blind, placebo-controlled, phase 3 pivotal trial including crossover vaccination after emergency authorization of Covid-19 vaccines. Adults aged ≥18 years were randomized to receive Ad26.COV2.S or placebo as a primary dose plus a booster dose at two months. The primary endpoint was vaccine efficacy against the first occurrence of molecularly-confirmed moderate to severe–critical Covid-19 with onset ≥14 days after booster vaccination in the per-protocol population. Key efficacy, safety, and immunogenicity endpoints were also assessed.ResultsThe double-blind phase enrolled 31,300 participants, 14,492 of whom received 2 doses and were evaluable for efficacy (per-protocol set, Ad26.COV2.S n=7484; placebo n=7008). Baseline demographics and characteristics were balanced. Vaccine efficacy was 75.2% (adjusted 95% CI, 54.6-87.3) against moderate to severe–critical Covid-19 and was similar against symptomatic infection (75.6% [55.5-99.9]). Efficacy was consistent across participants with and without comorbidities, and reached 93.7% (58.5-99.9) in the US. Vaccine efficacy against severe–critical Covid-19 was 100% (32.6-100.0; 0 vs 8 cases). The booster vaccine induced robust humoral responses and exhibited an acceptable safety profile.ConclusionsA homologous Ad26.COV2.S booster administered 2 months after primary single-dose vaccination in adults led to high vaccine efficacy, including against any symptomatic infection and SARS-CoV-2 variants prevalent during the study. (Funding: Janssen Research and Development and others; ENSEMBLE2 ClinicalTrials.gov number, NCT04614948.)
Direct DNA sequencing of ‘Candidatus Liberibacter asiaticus’ from Diaphorina citri, the Asian citrus psyllid, and its implications for citrus greening disease management
Authors: Higgins Steven Adam , Mann Marina , Heck Michelle 
Published: February 2022

AbstractThe Asian citrus psyllid, Diaphorina citri is an invasive insect 1 and a vector of ’Candidatus Liberibacter asiaticus’ (CLas), a bacterium whose growth in Citrus species results in citrus greening disease 2,3. Methods to enrich and sequence CLas from D. citri often rely on biased genome amplification 4 and nevertheless contain significant quantities of host DNA 5,6. To overcome these hurdles, we developed a simple pre-treatment DNase and filtration (hereafter PDF) protocol to directly sequence CLas and the complete, primarily uncultivable, microbiome from D. citri adults. The PDF protocol yielded CLas abundances upwards of 60% and enabled detection of 156 genetic variants in these strains compared to progenitor strains in Florida, which included prophage encoding regions with key functions in CLas pathogenesis, putative antibiotic resistance loci, and a single secreted effector. These variants suggest laboratory propagation of CLas may result in different phenotypic trajectories among laboratories, and may confound CLas physiology or therapeutic design and evaluation if these differences remain undocumented. Finally, we obtained genetic signatures affiliated with Citrus nuclear and organellar genomes, entomopathogenic fungal mitochondria, and commensal bacteria from laboratory-reared and field-collected D. citri adults. Hence, the PDF protocol can inform agricultural management strategies related to pathogen evolution 7, insect microbiome surveillance 8, antibiotic resistance screening 9, and gut content analysis 10.
Intraoperative electrical stimulation of the human dorsal spinal cord reveals a map of arm and hand muscle responses
Authors: McIntosh James R. , Joiner Evan. F. , Goldberg Jacob L. , Murray Lynda M. , Yasin Bushra , Mendiratta Anil , Karceski Steven C. , Thuet Earl , Modik Oleg , Shelkov Evgeny , Lombardi Joseph M. , Sardar Zeeshan M. , Lehman Ronald A. , Mandigo Christopher , Riew K. Daniel , Harel Noam Y. , Virk Michael S. , Carmel Jason B. 
Published: February 2022

AbstractWhile epidural stimulation of the lumbar spinal cord has emerged as a powerful modality for recovery of movement, how it should be targeted to the cervical spinal cord to activate arm and hand muscles is not well-understood, particularly in humans. We sought to map muscle responses to posterior epidural cervical spinal cord stimulation in humans. We hypothesized that lateral stimulation over the dorsal root entry zone would be most effective, and responses would be strongest in the muscles innervated by the stimulated segment. Twenty-five people undergoing clinically indicated cervical spine surgery were consented to map motor responses. During surgery, stimulation was performed in midline and lateral positions at multiple exposed segments; six arm and three leg muscles were recorded on each side of the body. Across all segments and muscles tested, lateral stimulation produced stronger muscle responses than midline despite similar latency and shape of responses. Muscles innervated at a cervical segment had the largest responses from stimulation at that segment, but responses were also observed in muscles innervated at other cervical segments and in leg muscles. The cervical responses were clustered in rostral (C4-C6) and caudal (C7-T1) cervical segments. Strong responses to lateral stimulation are likely due to the proximity of stimulation to afferent axons. Small changes in response sizes to stimulation of adjacent cervical segments argues for local circuit integration, and distant muscle responses suggest activation of long propriospinal connections. This map can help guide cervical stimulation to improve arm and hand function.New and noteworthyA map of muscle responses to cervical epidural stimulation during clinically indicated surgery revealed strongest activation when stimulating laterally compared to midline, and differences to be weaker than expected across different segments. In contrast, waveform shapes and latencies were most similar when stimulating midline and laterally indicating activation of overlapping circuitry. Thus, a map of the cervical spinal cord reveals organization and may help guide stimulation to activate arm and hand muscles strongly and selectively.Graphical abstract
Role of mucin gene for growth in Anas platyrynchos - a novel report
Authors: Murmu Anuj kumar , Pal Aruna , Debnath Manti , Chakraborty Argha , Pal Subhomoy , Banerjee Samiddha , Pal Abantika , Ghosh Nilotpal , Karmakar Utpal , Samanta Rajarshi 
Published: February 2022

AbstractMucin gene is expressed at the mucous membrane of the inner layer of the internal organs. Intestinal mucin 2 (MUC2), a major gel-forming mucin, represents a primary barrier component of mucus layers. This is the first report of role of mucin gene in growth traits in animals. In the current study, we had randomly studied Bengal ducks (Anas platyrynchos) reared from day old to 10 weeks of age under organized farm and studied the growth parameters as well as body weight and average daily body weight gain. We had characterized mucin gene for Bengal duck and observed glycosylation and EGF1 (EGF like domain signature) as important domain for growth traits in duck. We observed better expression profile for mucin gene in high growing ducks in comparison to that of lower growing ducks with real time PCR. Hence mucin gene may be employed as a marker for growth traits.
Group-walk, a rigorous approach to group-wise false discovery rate analysis by target-decoy competition
Authors: Freestone Jack , Short Temana , Noble William Stafford , Keich Uri 
Published: February 2022

AbstractTarget-decoy competition (TDC) is a commonly used method for false discovery rate (FDR) control in the analysis of tandem mass spectrometry data. This type of competitionbased FDR control has recently gained significant popularity in other fields after Barber and Candès laid its theoretical foundation in a more general setting that included the feature selection problem. In both cases, the competition is based on a head-to-head comparison between an (observed) target score and a corresponding decoy (knockoff) score. However, the effectiveness of TDC depends on whether the data is homogeneous, which is often not the case: in many settings, the data consists of groups with different score profiles or different proportions of true nulls. In such cases, applying TDC while ignoring the group structure often yields imbalanced lists of discoveries, where some groups might include relatively many false discoveries and other groups include relatively very few. On the other hand, as we show, the alternative approach of applying TDC separately to each group does not rigorously control the FDR.We developed Group-walk, a procedure that controls the FDR in the target-decoy / knockoff setting while taking into account a given group structure. Group-walk is derived from the recently developed AdaPT — a general framework for controlling the FDR with sideinformation. We show using simulated and real datasets that when the data naturally divides into groups with different characteristics Group-walk can deliver consistent power gains that in some cases are substantial. These groupings include the precursor charge state (4% more discovered peptides at 1% FDR threshold), the peptide length (3.6% increase) and the mass difference due to modifications (26% increase).Group-walk is available at https://cran.r-project.org/web/packages/groupwalk/index.html
Quantification of phosphonate drugs by 1H-31P HSQC shows that rats are better models of primate drug exposure than mice
Authors: Barekatain Yasaman , Khadka Sunada , Harris Kristen , Delacerda Jorge , Yan Victoria C. , Chen Ko-Chien , Pham Cong-Dat , Uddin Md. Nasir , Avritcher Rony , Eisenberg Eugene J. , Kalluri Raghu , Millward Steven W. , Muller Florian L. 
Published: February 2022

AbstractThe phosphonate group is a key pharmacophore in many anti-viral, anti-microbial, and anti-neoplastic drugs. Due to its high polarity and short retention time, detecting and quantifying such phosphonate-containing drugs with LC/MS-based methods is challenging and requires derivatization with hazardous reagents. Given the emerging importance of phosphonate-containing drugs, developing a practical, accessible, and safe method for their quantitation in pharmacokinetics (PK) studies is desirable. NMR-based methods are often employed in drug discovery but are seldom used for compound quantitation in PK studies. Here, we show that proton-phosphorous (1H-31P) heteronuclear single quantum correlation (HSQC) NMR allows for quantitation of the phosphonate-containing enolase inhibitor HEX in plasma and tissue at micromolar concentrations. Although mice were shown to rapidly clear HEX from circulation (over 95% in <1 hr), the plasma half-life of HEX was more than 1hr in rats and nonhuman primates. This slower clearance rate affords a significantly higher exposure of HEX in rat models compared to mouse models while maintaining a favorable safety profile. Similar results were observed for the phosphonate-containing antibiotic, fosfomycin. Our study demonstrates the applicability of the 1H-31P HSQC method to quantify phosphonate-containing drugs in complex biological samples and illustrates an important limitation of mice as preclinical model species for phosphonate-containing drugs.
Tension at intercellular junctions is necessary for accurate orientation of cell division in the epithelium plane
Authors: Lisica Ana , Fouchard Jonathan , Kelkar Manasi , Wyatt Tom P. J. , Duque Julia , Ndiaye Anne-Betty , Bonfanti Alessandra , Baum Buzz , Kabla Alexandre J. , Charras Guillaume T. 
Published: February 2022

AbstractThe direction in which a cell divides is set by the orientation of its mitotic spindle and is important for determining cell fate, controlling tissue shape and maintaining tissue architecture. Division perpendicular to the plane of the substrate can promote tissue stratification during development or wound healing, but also metastasis when orientation is aberrant. Much is known about the molecular mechanisms involved in setting the spindle orientation. However, less is known about the contribution of mechanical factors, such as tissue tension, in ensuring spindle orientation in the plane of the epithelium, despite epithelia being continuously subjected to mechanical stresses. Here, we used suspended epithelial monolayers devoid of extracellular matrix and subjected to varying levels of tissue tension to study the orientation of division relative to the tissue plane. We found that decreasing tissue tension by compressing the monolayers or by inhibiting myosin contractility leads to a higher frequency of out-of-plane divisions. Reciprocally, accurate in-plane division can be restored by increasing tissue tension by increasing cell contractility or by tissue stretching. By considering the full three-dimensional geometry of the epithelium, we show that spindles are sensitive to tissue tension, independently of cell shape, through its impact on the tension at subcellular surfaces. Overall, our data suggest that accurate spindle orientation in the plane of the epithelium necessitates the presence of a sufficiently large tension at intercellular junctions.Significance statementIn growing epithelia, divisions are typically oriented in the plane of the tissue to drive expansion. In some organs, divisions are then re-oriented so that they occur perpendicular to the epithelium plane to drive tissue stratification and cell differentiation. When uncontrolled, this switch in orientation can lead to defects in tissue organisation and, in cancer, likely contribute to metastasis. While much is known about the molecular mechanisms controlling mitotic spindle orientation, less is known about the role of mechanical factors. Here we use mechanical and chemical perturbations to show that mechanics plays a role in controlling the plane of division. Overall, our data suggest that the orientation of spindles in the epithelium plane requires sufficient tension across intercellular junctions.
Expanded Analysis of Pigmentation Genetics in UK Biobank
Authors: Pairo-Castineira Erola , Cornelissen Jaime , Rawlik Konrad , Canela-Xandri Oriol , Loftus Stacie K. , Pavan William J. , Brown Kevin M. , Tenesa Albert , Jackson Ian J. 
Published: February 2022

AbstractThe genetics of pigmentation is an excellent model for understanding gene interactions in a trait almost entirely unaffected by environment. We have analysed pigmentation phenotypes in UK Biobank using DISSECT, a tool which enables genome-wide association studies (GWAS) whilst accounting for relatedness between individuals, and thus allows a much larger cohort to be studied. We have increased the number of candidate genes associated with red and blonde hair colour, basal skin colour and tanning response to UV radiation. As previously described, we find almost all red hair individuals have two variantMC1Ralleles; exome sequence data expands the number of associated coding variants. Rare red-headed individuals with only a singleMC1Rvariant are enriched for an associated eQTL at theASIPgene. We find that females are most likely to self-report red or blonde hair, paler skin and less tanning ability than men, and that variants atKITLG, MC1R, OCA2andIRF4show significant sex differences in effect. After taking sex into account, pigmentation phenotypes are not correlated with sex hormone levels, except for tanning ability, which shows a positive correlation with testosterone in men. Across the UK there is a correlation between place of birth and hair colour; red hair being more common in the north and west, whilst blonde hair is more common in the east. Combining GWAS with transcriptome data to generate a transcriptome wide association study identifies candidate genes whose expression in skin or melanocytes shows association with pigmentation phenotypes. A comparison of candidates associated with different pigmentation phenotypes finds that candidates for blonde hair, but not skin colour, are enriched for skin and hair genes suggesting that it may be hair shape and structure that impacts hair colour, rather than the melanocyte/keratinocyte interaction.
Reproductive strategies in a complex of simultaneously hermaphroditic species, the Allolobophora chlorotica case study
Authors: Dupont L. , Audusseau H. , Porco D. , Butt K. R. 
Published: February 2022

AbstractAn in-depth knowledge of reproductive strategies is essential to understand the evolutionary history of species and their resulting patterns of taxonomic diversity. In particular, the study of life history traits related to reproduction could help to resolve the speciation patterns in the cryptic species complexes recently found in earthworms. Here, we carried out a parentage analysis in such a complex, the Allolobophora chlorotica aggregate. Using four nuclear microsatellite markers and a fragment of the cytochrome c oxidase subunit I mitochondrial gene we investigated (i) the mating strategies between individuals belonging to two divergent mitochondrial lineages (L2 and L3) that cannot be distinguished with nuclear markers and (ii) the reproductive isolation between lineages that are differentiated both at the mitochondrial and nuclear level (L2/L3 and L1). Among the 157 field collected individuals, 66 adults were used in cross-breeding experiments to form 22 trios based on their assignment to a mitochondrial lineage, and 453 obtained juveniles were genotyped. We showed that adults that mated with both their potential mates in the trio produced significantly more juveniles. In L2 and L3 crosses, a sex-specific pattern of reproduction characteristic to each lineage was observed, suggesting a possible conflict of interest between mating partners. In L2/L3 and L1 crosses, a high production of cocoons was counterbalanced by a low hatching rate, suggesting a post-zygotic reproductive isolation. Reproductive strategies are thus likely to contributed to the diversification of this complex of species and we advocate further studies on sexual selection and sex allocation in earthworms.