bluuebunny/crossref_metadata_2025_split huggingface dataset:
Older age bipolar disorder
Authors: Beunders Alexandra J.M. , Orhan Melis , Dols Annemiek 
Published: July 2023

Purpose of review
Older age bipolar disorder (OABD) refers to patients with bipolar disorder aged 50 years and over. There is a paucity of evidence-based guidelines specific to OABD, but in recent years, several studies have been published on OABD. The current review synthesizes previous literature (up to January 1, 2021) as well as most recent literature on OABD (since January 1, 2021).

Recent findings
This review covers the following themes: diagnosis and specifiers, clinical course, psychosocial functioning, cognition, physical comorbidities, and pharmacotherapy. On the basis of the latest data, specific clinical recommendations are proposed for each theme.

Summary
OABD forms a more complex subgroup of bipolar disorder, with an increased risk of cognitive deficits, physical comorbidities, impaired psychosocial functioning, and premature death. The distinctions between BD-I and BD-II and between EOBD and LOBD do not clinically represent relevant subtypes for OABD patients. Mental healthcare professionals should treat all OABD patients with an integrative care model that takes into account cognitive and physical comorbidities and that contains elements aimed at improvement of psychosocial functioning and quality of life. Older age itself should not be a reason to withhold lithium treatment. Future research should collect data on essential data domains using validated measurement scales.
Removing direct photocurrent artifacts in optogenetic connectivity mapping data via constrained matrix factorization
Authors: Antin Benjamin , Sadahiro Masato , Gajowa Marta , Triplett Marcus A. , Adesnik Hillel , Paninski Liam 
Published: July 2023

AbstractMonosynaptic connectivity mapping is crucial for building circuit-level models of neural computation. Two-photon optogenetic stimulation, when combined with whole-cell recordings, has the potential to map monosynaptic connectivity at an unprecedented scale. However, optogenetic mapping of nearby connections poses a challenge, due to stimulation artifacts. When the postsynaptic cell expresses opsin, optical excitation can directly induce current in the patched cell, confounding connectivity measurements. This problem is most severe in nearby cell pairs, where synaptic connectivity is often strongest. To overcome this problem, we developed a computational tool, Photocurrent Removal with Constraints (PhoRC). Our method is based on a constrained matrix factorization model which leverages the fact that photocurrent kinetics are consistent across repeated stimulations at similar laser power. We demonstrate on real and simulated data that PhoRC consistently removes photocurrents while preserving synaptic currents, despite variations in photocurrent kinetics across datasets. Our method allows the discovery of synaptic connections which would have been otherwise obscured by photocurrent artifacts, and may thus reveal a more complete picture of synaptic connectivity. PhoRC runs faster than real time and is available athttps://github.com/bantin/PhoRC.
Activity of natural occurring entomopathogenic fungi on nymphal and adult stage ofPhilaenus spumarius
Authors: Bodino N. , Barbera R. , Gonzalez-Mas N. , Demichelis S. , Bosco D. , Dolci P. 
Published: July 2023

ABSTRACTThe spittlebugPhilaenus spumarius(Hemiptera: Aphrophoridae) is the predominant vector ofXylella fastidiosa(Xanthomonadales: Xanthomonadaceae) in Apulia and Europe. Current control strategies of the insect vector rely on mechanical management of nymphal stages and insecticide application against adult populations. Entomopathogenic fungi (EPF) are biological control agents naturally attacking spittlebugs and may effectively reduce population levels of host species. Different experimental trials in controlled conditions have been performed to i) identify naturally occurring EPF onP. spumariusin Northwestern Italy, and ii) evaluate the potential for biocontrol of the isolated strains on both nymphal and adult stages of the spittlebug. Four EPF species were isolated from deadP. spumariuscadavers collected in semi-field conditions:Beauveria bassiana, Conidiobolus coronatus, Fusarium equisetiandLecanicillium aphanocladii. All the fungal isolates showed entomopathogenic potential against nymphal stages ofP. spumarius(≈ 45 % mortality), except forF. equiseti, in preliminary trials. No induced mortality was observed on the adult stage.Lecanicillium aphanocladiiwas the most promising fungus and its pathogenicity against spittlebug nymphs was further tested in different formulations (conidia vs blastospores) and with natural adjuvants. Blastospore formulation was the most effective in killing nymphal instars and reducing the emergence rate ofP. spumariusadults, reaching mortality levels (90%) similar to those of the commercial product Naturalis®, while no or adverse effect of natural adjuvants was recorded. The encouraging results of this study pave the way for testing EPF isolates againstP. spumariusin field conditions and find new environmentally friendly control strategies against insect vectors ofX. fastidiosa.
Distinct Functional States of Neutrophils by Actin Disassembly and NF-kB/STAT3 Signaling
Authors: Heineken Niko , Schumacher Jan C. , Exner Tarik , Neuenfeldt Friederike S. , Habicht Jüri , Kahlich Franz , Platzer Hadrian , Merle Uta , Renkawitz Tobias , Samstag Yvonne , Grieshaber-Bouyer Ricardo , Autenrieth Stella , Wabnitz Guido 
Published: July 2023

AbstractPolymorphonuclear neutrophils (PMNs) can differentiate into distinct states, which can either exacerbate or resolve inflammation. Our study shows that mice challenged with TLR agonists exhibited PMN differentiation along two major paths characterized by the expression of CCR5 or PD-L1. Similar differentiation was observed in the blood of severe COVID-19 patients and the synovial fluid of osteoarthritis patients. Prolongedin vitropriming of human PMNs modeled the differentiation paths. Actin disassembly favored CCR5 upregulation, while NF-kB activation stabilized the actin cytoskeleton and suppressed the development of CCR5+PMNs. Additionally, PD-L1 upregulation was triggered by STAT3 signaling and NF-kB activation. Functionally, CCR5 expressing PMNs were pro-NETotic, while PD-L1+PMNs showed immunosuppressive functions by inhibiting T cell proliferation via PD1. Together, PMN differentiation depended on the priming conditions, and the balance between actin disassembly and NF-kB/STAT3 activation translated the present micro-milieu into phenotypic and functional diversification of PMNs.SynopsisNeutrophils underwent phenotypical and functional diversification bothin vivoandin vitro. Actin disassembly led to the generation of CCR5highneutrophils with increased spontaneous NETosis, whereas NF-kB and STAT3 induced PD-L1 expression with T-cell suppressive properties as a deviation from the default pathway.PMN of mice challenged with TLR agonists develop two distinct phenotypes, CCR5highand PD-L1high.CCR5 and PD-L1-defined neutrophil phenotypes were found in blood of patients with severe COVID-19 and in the synovial fluid of osteoarthritis patients.In vitropriming induced a similar bifurcation of PMN phenotypes marked by either CCR5 or PD-L1.Actin disassembly preceded canonical development of CCR5+PMN.NF-kB halted actin disassembly by LPL regulation.During neutrophil priming, STAT3 aided NF-kB in the expression of PD-L1.Graphical abstract
Nucleolar detention of NONO shields DNA double-strand breaks from aberrant transcripts
Authors: Trifault Barbara , Mamontova Victoria , Cossa Giacomo , Ganskih Sabina , Wei Yuanjie , Hofstetter Julia , Bhandare Pranjali , Baluapuri Apoorva , Solvie Daniel , Ade Carsten P. , Gallant Peter , Wolf Elmar , Munschauer Mathias , Burger Kaspar 
Published: July 2023

ABSTRACTRNA-binding proteins (RBPs) stimulate the DNA damage response (DDR). The RBP NONO marks nuclear paraspeckles in unperturbed cells and undergoes poorly understood re-localisation to the nucleolus upon induction of DNA double-strand breaks (DSBs). Here we show that treatment with the topoisomerase-II inhibitor etoposide stimulates the production of RNA polymerase II-dependent, DNA damage-induced nucleolar antisense RNAs (diNARs) in human cells. diNARs originate from the nucleolar intergenic spacer and tether NONO to the nucleolus via its RRM1 domain. NONO occupancy at protein-coding gene promoters is reduced by etoposide, which attenuates pre-mRNA synthesis, enhances NONO binding to pre-mRNA transcripts and is accompanied by nucleolar detention of such transcripts. The depletion or mutation of NONO interferes with detention and prolongs DSB signaling. Together, we describe a nucleolar DDR pathway that shields NONO and aberrant transcripts from DSBs to promote DNA repair.
Swimming by spinning: spinning-top type rotations regularize sperm swimming into persistently symmetric paths in 3D
Authors: Ren Xiaomeng , Bloomfield-Gadêlha Hermes 
Published: July 2023

AbstractSperm modulate their flagellar symmetry to navigate through complex physico-chemical environments and achieve reproductive function. Yet it remains elusive how sperm swim forwards despite the inherent asymmetry of several components that constitutes the flagellar engine. Despite the critical importance of symmetry, or the lack of it, on sperm navigation and its physiological state, there is no methodology to date that can robustly detect the symmetry state of the beat in free-swimming sperm in 3D. How does symmetric progressive swimming emerge even for asymmetric beating, and how can beating (a)symmetry be inferred experimentally? Here, we numerically resolve the fluid mechanics of swimming around asymmetrically beating spermatozoa. This reveals that sperm spinning critically regularizes swimming into persistently symmetric paths in 3D, allowing sperm to swim forwards despite any imperfections on the beat. The sperm orientation in three-dimensions, and not the swimming path, can inform the symmetry state of the beat, eliminating the need of tracking the flagellum in 3D. We report a surprising correspondence between the movement of sperm and spinning-top experiments, indicating that the flagellum drives “spinning-top” type rotations during sperm swimming, and that this parallel is not a mere analogy. These results may prove essential in future studies on the role of (a)symmetry in spinning and swimming microorganisms and micro-robots, as body orientation detection has been vastly overlooked in favour of swimming path detection. Altogether, sperm rotation may provide a foolproof mechanism for forward propulsion and navigation in nature that would otherwise not be possible for flagella with broken symmetry.
Using UAV-based temporal spectral indices to dissect changes in the stay green trait in wheat
Authors: Yu Rui , Cao Xiaofeng , Liu Jia , Nie Ruiqi , Zhang Chuanliang , Yuan Meng , Huang Yanchuan , Liu Xinzhe , Zheng Weijun , Wang Changfa , Wu Tingting , Su Baofeng , Kang Zhensheng , Zeng Qingdong , Han Dejun , Wu Jianhui 
Published: July 2023

AbstractStay green (SG) in wheat, a beneficial trait for increasing yield and stress resistance, needs to be supported by analysis of the underlying genetic basis. Spectral reflectance indices (SIs) provide non-destructive tools to evaluate crop temporal senescence. However, few SI-based SG quantification pipelines for analyzing diverse wheat panels in the field are available. Here, we first applied SIs to monitor the senescence dynamics of 565 diverse wheat accessions from anthesis to maturation stages during two field seasons. Based on over 12,000 SIs data set, four SIs (NDVI, GNDVI, NDRE and OSAVI) were selected to develop relative stay green scores (RSGS) and the senescence of wheat populations occurs mainly at four developmental stages stage 1 (S1) to S4, accounting for the final SG indicators. A RSGS-based genome-wide association study identified 47 high-confidence quantitative trait loci (QTL) harboring 3,079 SNPs significantly associated with RSGS and 1,085 corresponding candidate genes in the two seasons; 15 QTL overlapped or were adjacent to known SG-related QTL or genes and the remaining QTL were novel. Finally, we selected three superior candidate genes (TraesCS6B03G0356400,TraesCS2B03G1299500, andTraesCS2A03G1081100) as examples by transcriptomes, gene annotation, and gene-based association analysis for further analysis and found that utilization of superior SG-related variation in China gradually increased following the Green Revolution. The study provides a useful reference for further SG-related gene discovery of favorable variations in diverse wheat panels.
Long-Distance Electron Transport in Multicellular Freshwater Cable Bacteria
Authors: Yang Tingting , Chavez Marko S. , Niman Christina M. , Xu Shuai , El-Naggar Mohamed Y. 
Published: July 2023

AbstractFilamentous multicellular cable bacteria perform centimeter-scale electron transport in a process that couples oxidation of an electron donor (sulfide) in deeper sediment to the reduction of an electron acceptor (oxygen or nitrate) near the surface. While this electric metabolism is prevalent in both marine and freshwater sediments, detailed electronic measurements of the conductivity previously focused on the marine cable bacteria (CandidatusElectrothrix), rather than freshwater cable bacteria, which form a separate genus (CandidatusElectronema) and contribute essential geochemical roles in freshwater sediments. Here, we characterize the electron transport characteristics ofCa.Electronema cable bacteria from Southern California freshwater sediments. Current-voltage measurements of intact cable filaments bridging interdigitated electrodes confirmed their persistent conductivity under a controlled atmosphere and the variable sensitivity of this conduction to air exposure. Electrostatic and conductive atomic force microscopies mapped out the characteristics of the cell envelope’s nanofiber network, implicating it as the conductive pathway in a manner consistent with previous findings in marine cable bacteria. Four-probe measurements of microelectrodes addressing intact cables demonstrated nanoampere currents up to 200 μm lengths at modest driving voltages, allowing us to quantify the nanofiber conductivity at 0.1 S/cm for freshwater cable bacteria filaments under our measurement conditions. Such a high conductivity can support the remarkable sulfide-to-oxygen electrical currents mediated by cable bacteria in sediments. These measurements expand the knowledgebase of long-distance electron transport to the freshwater niche while shedding light on underlying conductive network of cable bacteria.SignificanceCable bacteria are multicellular filaments composed of up-to-thousands of end-to-end cells and are found worldwide in both marine and freshwater sediments. Remarkably, these cells gain energy from a long-distance electron transport process that carries electrons generated by sulfide oxidation in deeper sediment layers to drive oxygen reduction near the sediment-water interface. This electric metabolism requires an unusually high electronic conductivity, previously thought impossible in natural biological materials. However, the underlying mechanism(s) remain poorly understood, and previous characterization of the conductivity largely focused on marine cable bacteria. Here, we characterize and quantify the electronic conductivity of freshwater cable bacteria from sediments in Southern California, with emphasis on the role of the conductive periplasmic fiber network in routing electron transport along cables.
Tandemly duplicatedMYBgenes specifically in the Phaseoleae lineage are functionally diverged in the regulation of anthocyanin biosynthesis
Authors: Ma Ruirui , Huang Wenxuan , Hu Quan , Tian Guo , An Jie , Fang Ting , Liu Jia , Hou Jingjing , Zhao Meixia , Sun Lianjun 
Published: July 2023

AbstractGene duplications have long been recognized as a driving force in the evolution of genes, giving rise to novel functions. The soybean genome is characterized by a large extent of duplicated genes. However, the extent and mechanisms of functional divergence among these duplicated genes in soybean remain poorly understood. In this study, we revealed that tandem duplication ofMYBgenes, which occurred specifically in the Phaseoleae lineage, exhibited a stronger purifying selection in soybean compared to common bean. To gain insights into the diverse functions of theseMYBgenes in anthocyanin biosynthesis, we examined the expression, transcriptional activity, metabolite, and evolutionary history of fourMYBgenes (GmMYBA5,GmMYBA2, GmMYBA1andGlyma.09g235000), which were presumably generated by tandem duplication in soybean. Our data revealed thatGlyma.09g235000had become a pseudogene, while the remaining threeMYBgenes exhibited strong transcriptional activation activity and promoted anthocyanin biosynthesis in different soybean tissues. Furthermore,GmMYBA5produced distinct compounds inNicotiana benthamianaleaves compared toGmMYBA2andGmMYBA1due to variations in their DNA binding domains. The lower expression of anthocyanin related genes inGmMYBA5resulted in lower levels of anthocyanins compared toGmMYBA2andGmMYBA1. Metabolomics analysis further demonstrated the diverse and differential downstream metabolites, suggesting their functional divergence in metabolites following gene duplication. Together, our data provided evidence of functional divergence within theMYBgene cluster following tandem duplication, which shed light on the potential evolutionary direction of gene duplications during legume evolution.
The Patent and Literature Antibody Database (PLAbDab): an evolving reference set of functionally diverse, literature-annotated antibody sequences and structures
Authors: Abanades Brennan , Olsen Tobias H. , Raybould Matthew I. J. , Aguilar-Sanjuan Broncio , Wong Wing Ki , Georges Guy , Bujotzek Alexander , Deane Charlotte M. 
Published: July 2023

ABSTRACTAntibodies are key proteins of the adaptive immune system, and there exists a large body of academic literature and patents dedicated to their study and concomitant conversion into therapeutics, diagnostics, or reagents. These documents often contain extensive functional characterisations of the sets of antibodies the describe. However, leveraging these heterogeneous reports, for example to offer insights into the properties of query antibodies of interest, is currently challenging as there is no central repository through which this wide corpus can be mined by sequence or structure.Here, we present PLAbDab (the Patent and Literature Antibody Database), a self-updating repository containing over 150,000 paired antibody sequences and 3D structural models, of which over 65,000 are unique. Each entry in the database also contains the title and authors of its literature source. Here we describe the methods used to extract, filter, pair, and model the antibodies in PLAbDab, and showcase how PLAbDab can be searched by sequence, structure, or keyword.PLAbDab uses include annotating query antibodies with potential antigen information from similar entries, analysing structural models of existing antibodies to identify modifications that could improve their properties, and compiling bespoke datasets of antibody sequences/structures known to bind to a specific antigen. PLAbDab is freely available via Github (https://github.com/oxpig/PLAbDab) and as a searchable webserver (https://opig.stats.ox.ac.uk/webapps/plabdab/).
Prospective multicenter validation of a new laboratory workflow integrating the free light chains kappa quotient in CSF analysis-Protocol of the ORCAS study
Authors: Dressel Alexander , Hannich Malte Johannes , Süße Marie 
Published: July 2023

ABSTRACTIntroductionFree light chain kappa (FLCκ) are a newer sensitive biomarker to detect intrathecal immunoglobulin synthesis. Here we report the study protocol of the ORCAS study which will evaluate a novel laboratory work flow recently proposed including FLCκ analysis simplifying cerebrospinal fluid (CSF) analysis.MethodsThe ORCAS study is a prospective multicenter diagnostic biomarker study across at least 4 study sites. The study protocol does not specify which assays should be applied in the participating laboratories to detect oligoclonal bands (OCB) or measure FLCκ or Ig synthesis to represent real world data. Primary outcome parameter is the sensitivity and negative predictive value of the absence of local FLCκ synthesis for the absence of intrathecal synthesis according to OCB and/or intrathecal IgG, IgA, IgM synthesis in quotient diagrams. The reference range of FLCκ will be indicated by the FLCκ quotient diagram. This study was designed according to the STARD criteria.PerspectiveThe establishment of a newer biomarker in routine practice is associated with significant difficulties, such as the inconsistent comparability of different measurement platforms, the establishment of suitable cut-offs or insufficient knowledge regarding sensitivity and specificity of the biomarker. If the ORCAS study objective is achieved, the use of the proposed workflow integrating FLCκ analysis in routine practice in CSF diagnostics could help to better characterize the intraindividual and disease-specific intrathecal humoral immune response in a resource-efficient manner.
Effectiveness, barriers, and facilitating factors of strategies for active delabeling of patients with penicillin allergy labels: a systematic review protocol
Authors: Nürnberg Hannah , Khatamzas Elham , Denkinger Claudia M. , Krause Tabea , Oetken Lars , Rauer Sophie , Rapp Amelie , Hoppe-Tichy Torsten , Morath Benedict 
Published: July 2023

ABSTRACTIntroductionUp to 15 % of adult patients in the clinical setting report to be allergic to penicillin. However, in most cases penicillin allergy is not confirmed. Due to the negative aspects associated with erroneous penicillin allergy, the implementation of active delabeling processes for penicillin allergy is an important part of antibiotic stewardship programs. Depending on the clinical setting, different factors need to be considered during implementation. This review examines the effectiveness of different delabeling interventions and summarizes components and structures that facilitate, support, or constrain structured penicillin allergy delabeling.Methods and analysisThis review will adhere to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA). The Databases MEDLINE (via PubMed), EMBASE, and Cochrane Library were searched for studies reporting on any intervention to identify, assess, or rule out erroneous penicillin allergy. Study design, intervention type, professional groups involved, effectiveness, limitations, barriers, facilitating factors, clinical setting, and associated regulatory factors will be extracted and analyzed. Two independent reviewers will perform the screening process and data extraction. Discordant decisions will be resolved through review by a third reviewer. Bias assessment of the individual studies will be performed using the Newcastle Ottawa Scale.Ethics and disseminationBecause individual patient-related data is not analyzed, an ethical approval is not required. The review will be published in a peer-reviewed scientific journal.STRENGHTS AND LIMITATIONS OF THIS STUDY-The systematic review will adhere to the PRISMA guidelines.-A wide search strategy is used and the search will be conducted on three major databases.-The search is focused on studies reporting on facilitators and barriers for implementation as well as effectiveness of penicillin allergy delabeling interventions.-Data extraction will be performed using an established second look process.-Risk for bias in the individual studies as well as external validity is assessed using an established checklist (Newcastle Ottawa Scale).