bluuebunny/crossref_metadata_2025_split huggingface dataset:
Assimilation of Groundwater Level and Soil Moisture Data in an Integrated Land Surface‐Subsurface Model for Southwestern Germany
Authors: Hung Ching Pui , Schalge Bernd , Baroni Gabriele , Vereecken Harry , Hendricks Franssen Harrie‐Jan 
Published: June 2022

AbstractIntegrated terrestrial system models predict the coupled water, energy and biogeochemical cycles. Simulations with these models are affected by uncertainties of model parameters, initial and boundary conditions, atmospheric forcings and the biophysical processes. Data assimilation (DA) can quantify and reduce the uncertainty. This has been tested intensively for single compartment models, but far less for integrated models with multiple compartments. We constructed a virtual reality (VR) with a coupled land surface‐subsurface model under the Terrestrial Systems Modeling Platform, which mimics the Neckar catchment in southern Germany. Soil moisture and groundwater level (GWL) data extracted from the simulated VR are used as measurements to be assimilated with state‐only/state‐hydraulic parameter estimation. Soil moisture DA improves soil moisture characterization in the vertical profile and the neighboring grid cells, with a 40 ∼ 60% reduction of root mean square error (RMSE) over the observation points. In spite of a small ensemble size of 64 members, assimilating soil moisture data improved saturated hydraulic conductivity estimation around the measurement locations. The characterization of evapotranspiration and river discharge only show limited improvements (1% at observation points and less than 0.1% in RMSE at 3 selected gauge locations respectively). GWL DA not only improves the GWL characterization (76 ∼ 88% RMSE reduction at observation locations) but also soil moisture for some cases. In addition, a clear improvement in GWL characterization is observed up to 8 km from the observations, and updating the model states of the saturated zone only instead of the complete domain gives better performance.
Re‐Evaluation of Low Cloud Amount Relationships With Lower‐Tropospheric Stability and Estimated Inversion Strength
Authors: Cutler Lauren , Brunke Michael A. , Zeng Xubin 
Published: June 2022

AbstractLower‐tropospheric stability (LTS) and estimated inversion strength (EIS) have a widely accepted relationship with low cloud amount and are key observational foundations for understanding and modeling low‐level stratiform clouds. Using the updated surface‐based and satellite cloud data, we find that low cloud amount is not as strongly correlated with LTS, and not as sensitive to LTS, as established in the past. EIS does not provide a stronger correlation with low cloud amount than LTS over all eight regions (including the midlatitudes). Further analyzing the relationships between LTS and EIS with different types of low clouds, we find that there is a strong correlation of LTS and EIS with stratocumulus only. This explains the weaker correlation of low cloud fraction (including cumulus, stratocumulus, and stratus) to both LTS and EIS. These results also suggest the need to re‐evaluate these relationships in Earth system models.
Hyaluronan synthase 2, a target of miR-200c, promotes carbon tetrachloride-induced acute and chronic liver inflammation via regulation of CCL3 and CCL4
Authors: Kim Sun Myoung , Song Ga Yeon , Shim Aeri , Lee Jee Hyung , Eom Cheol Bin , Liu Cheng , Yang Yoon Mee , Seki Ekihiro 
Published: June 2022

AbstractLiver fibrosis occurs during wound healing after repeated liver injury and is characterized by extensive extracellular matrix deposition. We previously identified hyaluronan synthase 2 (HAS2) as a driver of liver fibrosis and hepatic stellate cell (HSC) activation. Developing strategies to suppress HSC activation is key to alleviating liver fibrosis, and HAS2 is an attractive candidate for intervention. To gain insight into the molecular function of HAS2, we investigated its posttranscriptional regulation. We found that miR-200c directly targets the 3’ untranslated regions of HAS2. Moreover, miR-200c and HAS2 were inversely expressed in fibrotic human and mouse livers. After establishing the direct interaction between miR-200c and HAS2, we investigated the functional outcome of regulating HAS2 expression in three murine models: CCl4-induced acute liver injury, CCl4-induced chronic liver fibrosis, and bile duct ligation-induced liver fibrosis. Hepatic Has2 expression was induced by acute and chronic CCl4 treatment. In contrast, miR-200c expression was decreased after CCl4 treatment. HSC-specific Has2 deletion reduced the expression of inflammatory markers and infiltration of macrophages in the models. Importantly, hyaluronidase-2 (HYAL2) but not HYAL1 was overexpressed in fibrotic human and murine livers. HYAL2 is an enzyme that can cleave the extracellular matrix component hyaluronan. We found that low-molecular-weight hyaluronan stimulated the expression of inflammatory genes. Treatment with the HA synthesis inhibitor 4-methylumbelliferone alleviated bile duct ligation-induced expression of these inflammatory markers. Collectively, our results suggest that HAS2 is negatively regulated by miR-200c and contributes to the development of acute liver injury and chronic liver inflammation via hyaluronan-mediated immune signaling.
Prognostic accuracy and clinical utility of psychometric instruments for individuals at clinical high-risk of psychosis: a systematic review and meta-analysis
Authors: Oliver Dominic , Arribas Maite , Radua Joaquim , Salazar de Pablo Gonzalo , De Micheli Andrea , Spada Giulia , Mensi Martina Maria , Kotlicka-Antczak Magdalena , Borgatti Renato , Solmi Marco , Shin Jae Il , Woods Scott W. , Addington Jean , McGuire Philip , Fusar-Poli Paolo 
Published: June 2022

AbstractAccurate prognostication of individuals at clinical high-risk for psychosis (CHR-P) is an essential initial step for effective primary indicated prevention. We aimed to summarise the prognostic accuracy and clinical utility of CHR-P assessments for primary indicated psychosis prevention. Web of Knowledge databases were searched until 1st January 2022 for longitudinal studies following-up individuals undergoing a psychometric or diagnostic CHR-P assessment, reporting transition to psychotic disorders in both those who meet CHR-P criteria (CHR-P + ) or not (CHR-P−). Prognostic accuracy meta-analysis was conducted following relevant guidelines. Primary outcome was prognostic accuracy, indexed by area-under-the-curve (AUC), sensitivity and specificity, estimated by the number of true positives, false positives, false negatives and true negatives at the longest available follow-up time. Clinical utility analyses included: likelihood ratios, Fagan’s nomogram, and population-level preventive capacity (Population Attributable Fraction, PAF). A total of 22 studies (n = 4 966, 47.5% female, age range 12–40) were included. There were not enough meta-analysable studies on CHR-P diagnostic criteria (DSM-5 Attenuated Psychosis Syndrome) or non-clinical samples. Prognostic accuracy of CHR-P psychometric instruments in clinical samples (individuals referred to CHR-P services or diagnosed with 22q.11.2 deletion syndrome) was excellent: AUC = 0.85 (95% CI: 0.81–0.88) at a mean follow-up time of 34 months. This result was driven by outstanding sensitivity (0.93, 95% CI: 0.87–0.96) and poor specificity (0.58, 95% CI: 0.50–0.66). Being CHR-P + was associated with a small likelihood ratio LR + (2.17, 95% CI: 1.81–2.60) for developing psychosis. Being CHR-P- was associated with a large LR- (0.11, 95%CI: 0.06−0.21) for developing psychosis. Fagan’s nomogram indicated a low positive (0.0017%) and negative (0.0001%) post-test risk in non-clinical general population samples. The PAF of the CHR-P state is 10.9% (95% CI: 4.1–25.5%). These findings consolidate the use of psychometric instruments for CHR-P in clinical samples for primary indicated prevention of psychosis. Future research should improve the ability to rule in psychosis risk.
Ultra-rare and common genetic variant analysis converge to implicate negative selection and neuronal processes in the aetiology of schizophrenia
Authors: Akingbuwa Wonuola A. , Hammerschlag Anke R. , Bartels Meike , Nivard Michel G. , Middeldorp Christel M. 
Published: June 2022

AbstractBoth common and rare genetic variants (minor allele frequency >1% and <0.1% respectively) have been implicated in the aetiology of schizophrenia. In this study, we integrate single-cell gene expression data with publicly available Genome-Wide Association Study (GWAS) and exome sequenced data in order to investigate in parallel, the enrichment of common and (ultra-)rare variants related to schizophrenia in several functionally relevant gene-sets. Four types of gene-sets were constructed 1) protein-truncating variant (PTV)-intolerant (PI) genes 2) genes expressed in brain cell types and neurons ascertained from mouse and human brain tissue 3) genes defined by synaptic function and location and 4) intersection genes, i.e., PI genes that are expressed in the human and mouse brain cell gene-sets. We show that common as well as ultra-rare schizophrenia-associated variants are overrepresented in PI genes, in excitatory neurons from the prefrontal cortex and hippocampus, medium spiny neurons, and genes enriched for synaptic processes. We also observed stronger enrichment in the intersection genes. Our findings suggest that across the allele frequency spectrum, genes and genetic variants likely to be under stringent selection, and those expressed in particular brain cell types, are involved in the same biological pathways influencing the risk for schizophrenia.
Functional RECAP (REpair CAPacity) assay identifies homologous recombination deficiency undetected by DNA-based BRCAness tests
Authors: Meijer Titia G. , Nguyen Luan , Van Hoeck Arne , Sieuwerts Anieta M. , Verkaik Nicole S. , Ladan Marjolijn M. , Ruigrok-Ritstier Kirsten , van Deurzen Carolien H. M. , van de Werken Harmen J. G. , Lips Esther H. , Linn Sabine C. , Memari Yasin , Davies Helen , Nik-Zainal Serena , Kanaar Roland , Martens John W. M. , Cuppen Edwin , Jager Agnes , van Gent Dik C. 
Published: June 2022

AbstractGermline BRCA1/2 mutation status is predictive for response to Poly-[ADP-Ribose]-Polymerase (PARP) inhibitors in breast cancer (BC) patients. However, non-germline BRCA1/2 mutated and homologous recombination repair deficient (HRD) tumors are likely also PARP-inhibitor sensitive. Clinical validity and utility of various HRD biomarkers are under investigation. The REpair CAPacity (RECAP) test is a functional method to select HRD tumors based on their inability to form RAD51 foci. We investigated whether this functional test defines a similar group of HRD tumors as DNA-based tests. An HRD enriched cohort (n = 71; 52 primary and 19 metastatic BCs) selected based on the RECAP test (26 RECAP-HRD; 37%), was subjected to DNA-based HRD tests (i.e., Classifier of HOmologous Recombination Deficiency (CHORD) and BRCA1/2-like classifier). Whole genome sequencing (WGS) was carried out for 38 primary and 19 metastatic BCs. The RECAP test identified all bi-allelic BRCA deficient samples (n = 15) in this cohort. RECAP status partially correlated with DNA-based HRD test outcomes (70% concordance for both RECAP-CHORD and RECAP-BRCA1/2-like classifier). RECAP selected additional samples unable to form RAD51 foci, suggesting that this functional assay identified deficiencies in other DNA repair genes, which could also result in PARP-inhibitor sensitivity. Direct comparison of these HRD tests in clinical trials will be required to evaluate the optimal predictive test for clinical decision making.
Cardiovascular risk of gonadotropin-releasing hormone antagonist versus agonist in men with prostate cancer: an observational study in Taiwan
Authors: Shao Yu-Hsuan Joni , Hong Jian-Hua , Chen Chun-Kai , Huang Chao-Yuan 
Published: June 2022

Abstract
Background
The impact of gonadotropin-releasing hormone (GnRH) antagonist and agonist (GnRHa) treatment on cardiovascular disease (CVD) risk in prostate cancer (PCa) remains inconclusive due to conflicting findings. We compared the effects of GnRH antagonist and GnRHa treatments on CVD risk in patients with PCa and pre-existing CVD, in a Taiwan population-based database.

Methods
We assessed the risk of major adverse CV events (MACE: ischemic heart disease [IHD], stroke, congestive heart failure [CHF] or all cause deaths) and composite CV events (IHD, stroke, CHF or CV deaths) occurring ≥90 days after androgen deprivation therapy (ADT) initiation in patients with PCa after 90 days of treatment with either GnRH antagonist (degarelix; n = 499) or GnRHa (goserelin, leuprolide, triptorelin; n = 15,127). Patients identified with pre-existing CVD had received cardiac therapy for IHD, reported a stroke or CHF within a year before ADT initiation. Adjusted hazard ratios (aHR) and 95% confidence interval (CI) were obtained for MACE and composite CV events risk after adjusting for age, baseline status of diabetes, hypertension and treatments received.

Results
All GnRH antagonist-treated patients showed lower risk of composite CV events than the GnRHa-treated patients. The lower composite CV events risk associated with GnRH antagonist was also observed in patients with metastasis at diagnosis (aHR 0.16; 95% CI, 0.04–0.38; p = 0.013) and those receiving ADT for more than six months (aHR 0.30; 95% CI, 0.16–0.54; p < 0.0001). In patients with pre-existing CVD, the MACE risk was 33% lower (aHR 0.67; 95% CI, 0.46–0.96; p = 0.0299) and composite CV events risk was 84% lower (aHR 0.16; 95% CI, 0.05–0.50; p = 0.0017) in GnRH antagonist-treated than the GnRHa-treated patients.

Conclusions
In patients with PCa and pre-existing CVD, GnRH antagonist use was associated with lower risks for composite CV events and MACE compared with GnRHa.
Identification of cerebrospinal fluid and serum metabolomic biomarkers in first episode psychosis patients
Authors: Shang Pei , Ho Ada Man-Choi , Tufvesson-Alm Maximilian , Lindberg Daniel R. , Grant Caroline W. , Orhan Funda , Eren Feride , Bhat Maria , Engberg Göran , Schwieler Lilly , Fatouros-Bergman Helena , Imbeault Sophie , Iverson Ryan M. , Dasari Surendra , Piehl Fredrik , Cervenka Simon , Sellgren Carl M. , Erhardt Sophie , Choi Doo-Sup 
Published: June 2022

AbstractPsychotic disorders are currently diagnosed by examining the patient’s mental state and medical history. Identifying reliable diagnostic, monitoring, predictive, or prognostic biomarkers would be useful in clinical settings and help to understand the pathophysiology of schizophrenia. Here, we performed an untargeted metabolomics analysis using ultra-high pressure liquid chromatography coupled with time-of-flight mass spectroscopy on cerebrospinal fluid (CSF) and serum samples of 25 patients at their first-episode psychosis (FEP) manifestation (baseline) and after 18 months (follow-up). CSF and serum samples of 21 healthy control (HC) subjects were also analyzed. By comparing FEP and HC groups at baseline, we found eight CSF and 32 serum psychosis-associated metabolites with non-redundant identifications. Most remarkable was the finding of increased CSF serotonin (5-HT) levels. Most metabolites identified at baseline did not differ between groups at 18-month follow-up with significant improvement of positive symptoms and cognitive functions. Comparing FEP patients at baseline and 18-month follow-up, we identified 20 CSF metabolites and 90 serum metabolites that changed at follow-up. We further utilized Ingenuity Pathway Analysis (IPA) and identified candidate signaling pathways involved in psychosis pathogenesis and progression. In an extended cohort, we validated that CSF 5-HT levels were higher in FEP patients than in HC at baseline by reversed-phase high-pressure liquid chromatography. To conclude, these findings provide insights into the pathophysiology of psychosis and identify potential psychosis-associated biomarkers.
Vapor phase polymerization of Ag QD-embedded PEDOT film with enhanced thermoelectric and antibacterial properties
Authors: Shi Wei , Yao Qin , Donghui Wang , Qu Sanyin , Chen Yanling , Lee Kyu Hyoung , Chen Lidong 
Published: June 2022

AbstractNonferric oxidant precursors have the unique advantage of directly polymerizing poly(3,4-ethylenedioxythiophene) (PEDOT)-inorganic composites. However, due to limited solubility and unmatched oxidation potentials, most oxidants only produce powders or porous materials. To obtain high-quality films with improved homogeneity and controllable particle sizes, the oxidants should be adaptable to high-standard PEDOT film fabrication techniques such as vapor phase polymerization (VPP). In this work, we discovered for the first time a nonferric metal salt suitable for the VPP process. With the addition of an Fe(III) salt to stabilize the reaction and adjust the oxidant ratio, micron-thick antibacterial S-PEDOT-Ag quantum dot (QD) composite films with tunable Ag wt% can be synthesized in one facile step. With a low Ag loading of ~0.2 wt%, the film exhibited an optimized power factor of 63.1 μW/mK2, which is among the highest values thus far reported for PEDOT-metal composites. Increase of the Ag(I) concentration in the precursor to a certain level may lead to minor decomposition of the polymer followed by the formation of Ag2S particles.
Electron-phonon interactions in halide perovskites
Authors: Yamada Yasuhiro , Kanemitsu Yoshihiko 
Published: June 2022

AbstractStrong electron-phonon interactions are frequently considered the origin of the unique electrical and optical properties of lead halide perovskites. Electron-phonon interactions induce the formation of a polaron, which is a charge carrier dressed with a phonon cloud. The details of polaron formation are crucial for carrier transport since polaron formation leads to a larger effective mass of a carrier. Several mechanisms have been proposed regarding the physics of polaron formation in halide perovskites, but the details are still under active debate. While the Fröhlich interaction plays an essential role in ionic crystals, we also need to consider the strong phonon anharmonicity of halide perovskites that may lead to the formation of an unconventional polaron. In this review article, we discuss the uniqueness of perovskite semiconductors from the viewpoint of electron-phonon interactions. We review the experimental results and the proposed models concerning the effective carrier mass and carrier mobility. Finally, we briefly explain two physical phenomena related to strong electron-phonon interactions: strong anti-Stokes photoluminescence and slow hot-carrier cooling.
Extremely confined gap plasmon modes: when nonlocality matters
Authors: Boroviks Sergejs , Lin Zhan-Hong , Zenin Vladimir A. , Ziegler Mario , Dellith Andrea , Gonçalves P. A. D. , Wolff Christian , Bozhevolnyi Sergey I. , Huang Jer-Shing , Mortensen N. Asger 
Published: June 2022

AbstractHistorically, the field of plasmonics has been relying on the framework of classical electrodynamics, with the local-response approximation of material response being applied even when dealing with nanoscale metallic structures. However, when the confinement of electromagnetic radiation approaches atomic scales, mesoscopic effects are anticipated to become observable, e.g., those associated with the nonlocal electrodynamic surface response of the electron gas. Here, we investigate nonlocal effects in propagating gap surface plasmon modes in ultrathin metal–dielectric–metal planar waveguides, exploiting monocrystalline gold flakes separated by atomic-layer-deposited aluminum oxide. We use scanning near-field optical microscopy to directly access the near-field of such confined gap plasmon modes and measure their dispersion relation via their complex-valued propagation constants. We compare our experimental findings with the predictions of the generalized nonlocal optical response theory to unveil signatures of nonlocal damping, which becomes appreciable for few-nanometer-sized dielectric gaps.
A synaptomic analysis reveals dopamine hub synapses in the mouse striatum
Authors: Paget-Blanc Vincent , Pfeffer Marlene E. , Pronot Marie , Lapios Paul , Angelo Maria-Florencia , Walle Roman , Cordelières Fabrice P. , Levet Florian , Claverol Stéphane , Lacomme Sabrina , Petrel Mélina , Martin Christelle , Pitard Vincent , De Smedt Peyrusse Véronique , Biederer Thomas , Perrais David , Trifilieff Pierre , Herzog Etienne 
Published: June 2022

AbstractDopamine transmission is involved in reward processing and motor control, and its impairment plays a central role in numerous neurological disorders. Despite its strong pathophysiological relevance, the molecular and structural organization of the dopaminergic synapse remains to be established. Here, we used targeted labelling and fluorescence activated sorting to purify striatal dopaminergic synaptosomes. We provide the proteome of dopaminergic synapses with 57 proteins specifically enriched. Beyond canonical markers of dopamine neurotransmission such as dopamine biosynthetic enzymes and cognate receptors, we validated 6 proteins not previously described as enriched. Moreover, our data reveal the adhesion of dopaminergic synapses to glutamatergic, GABAergic or cholinergic synapses in structures we named “dopamine hub synapses”. At glutamatergic synapses, pre- and postsynaptic markers are significantly increased upon association with dopamine synapses. Dopamine hub synapses may thus support local dopaminergic signalling, complementing volume transmission thought to be the major mechanism by which monoamines modulate network activity.
Establishment of mouse model of inherited PIGO deficiency and therapeutic potential of AAV-based gene therapy
Authors: Kuwayama Ryoko , Suzuki Keiichiro , Nakamura Jun , Aizawa Emi , Yoshioka Yoshichika , Ikawa Masahito , Nabatame Shin , Inoue Ken-ichi , Shimmyo Yoshiari , Ozono Keiichi , Kinoshita Taroh , Murakami Yoshiko 
Published: June 2022

AbstractInherited glycosylphosphatidylinositol (GPI) deficiency (IGD) is caused by mutations in GPI biosynthesis genes. The mechanisms of its systemic, especially neurological, symptoms are not clarified and fundamental therapy has not been established. Here, we report establishment of mouse models of IGD caused by PIGO mutations as well as development of effective gene therapy. As the clinical manifestations of IGD are systemic and lifelong lasting, we treated the mice with adeno-associated virus for homology-independent knock-in as well as extra-chromosomal expression of Pigo cDNA. Significant amelioration of neuronal phenotypes and growth defect was achieved, opening a new avenue for curing IGDs.