bluuebunny/crossref_metadata_2025_split huggingface dataset:
Small molecule drug development for rare genodermatoses – evaluation of the current status in epidermolysis bullosa
Authors: Wally Verena , Reisenberger Manuela , Kitzmüller Sophie , Laimer Martin 
Published: October 2020

Abstract
Background
Hereditary epidermolysis bullosa (EB) comprises a heterogeneous group of rare genodermatoses, which are caused by mutations in genes involved in the maintenance of the structural and functional integrity of dermo-epidermal adhesion in various stratified epithelia. In severe variants, generalized skin disease, extracutaneous manifestations and multi-organ involvement cause considerable morbidity and mortality. Causal and early treatment by re-expression of a respective mutated gene is the major long-term goal in therapy development. However, characterization and targeted modulation of pathogenic molecular cascades in EB also holds great promise as a symptom-relieving approach to ameliorate phenotype, complications and quality of life. Small molecules are chemical structures of less than 900 Da that can diffuse across cell membranes and interfere with target biomolecules, thus influencing their function at different levels. They constitute the vast majority of active components of all approved drugs.

Methods
We performed PubMed and Google Scholar search for publications and screened FDA- and EMA-hosted clinical trial registries to identify studies using small molecule-based drugs for epidermolysis bullosa. Upon detailed analysis this resulted in the identification of a total of 84 studies.

Results
We identified 52 publications and 32 registered trials that investigate small molecules for their safety and efficacy as treatment for different aspects of epidermolysis bullosa. Further, a total of 38 different small molecules clinically used in EB were found. Most frequent outcome measures concerned wound healing, reduction in blister numbers, as well as reduction of itch and pain, predominantly for EBS and RDEB.

Conclusion
We provide a comprehensive summary of the current status of clinical small molecule development for EB and discuss prospects and limitations in orphan drug development for rare conditions like EB.
Coping with Wolf-Hirschhorn syndrome: quality of life and psychosocial features of family carers
Authors: Berrocoso Sarah , Amayra Imanol , Lázaro Esther , Martínez Oscar , López-Paz Juan Francisco , García Maitane , Pérez Manuel , Al-Rashaida Mohammad , Rodríguez Alicia Aurora , Luna Paula Maria , Pérez-Núñez Paula , Blanco Raquel , Nevado Julián 
Published: October 2020

Abstract
Background
Wolf-Hirschhorn Syndrome (WHS) is a rare, congenital disease characterized by a distinctive facial phenotype, seizures, intellectual disability and developmental delay, and pre and postnatal growth requiring lifelong care. The psychosocial status of the family caregivers of children diagnosed with WHS is unknown. This study aims to characterize the sociodemographic and psychosocial profile of WHS caregivers and analyze how these variables impact their quality of life (QoL) and well-being.

Results
The sociodemographic and clinical profile of 22 Spanish caregivers of children with WHS and the characteristics of those affected have been described. Significant relationships were found between sociodemographic and psychosocial characteristics among caregivers. The impact on the parents’ QoL and negative relationship with the symptomatology were assessed. The use of engagement strategies such as problem focused coping was associated with improved psychological QoL and social support.

Conclusions
WHS caregivers share similarities in their profile and needs with caregivers of children with other rare diseases. Pychosocial support groups involving parents caring for children with the same disease could improve caregivers’ well-being and QoL by strengthening their social support network and using positive coping styles.
Modeling the β-secretase cleavage site and humanizing amyloid-beta precursor protein in rat and mouse to study Alzheimer’s disease
Authors: Serneels Lutgarde , T’Syen Dries , Perez-Benito Laura , Theys Tom , Holt Matthew G. , De Strooper Bart 
Published: October 2020

Abstract
Background
Three amino acid differences between rodent and human APP affect medically important features, including β-secretase cleavage of APP and Aβ peptide aggregation (De Strooper et al., EMBO J 14:4932-38, 1995; Ueno et al., Biochemistry 53:7523-30, 2014; Bush, 2003, Trends Neurosci 26:207–14). Most rodent models for Alzheimer’s disease (AD) are, therefore, based on the human APP sequence, expressed from artificial mini-genes randomly inserted in the rodent genome. While these models mimic rather well various biochemical aspects of the disease, such as Aβ-aggregation, they are also prone to overexpression artifacts and to complex phenotypical alterations, due to genes affected in or close to the insertion site(s) of the mini-genes (Sasaguri et al., EMBO J 36:2473-87, 2017; Goodwin et al., Genome Res 29:494-505, 2019). Knock-in strategies which introduce clinical mutants in a humanized endogenous rodent APP sequence (Saito et al., Nat Neurosci 17:661-3, 2014) represent useful improvements, but need to be compared with appropriate humanized wildtype (WT) mice.

Methods
Computational modelling of the human β-CTF bound to BACE1 was used to study the differential processing of rodent and human APP. We humanized the three pivotal residues we identified G676R, F681Y and R684H (labeled according to the human APP770 isoform) in the mouse and rat genomes using a CRISPR-Cas9 approach. These new models, termed mouse and rat Apphu/hu, express APP from the endogenous promotor. We also introduced the early-onset familial Alzheimer’s disease (FAD) mutation M139T into the endogenous Rat Psen1 gene.

Results
We show that introducing these three amino acid substitutions into the rodent sequence lowers the affinity of the APP substrate for BACE1 cleavage. The effect on β-secretase processing was confirmed as both humanized rodent models produce three times more (human) Aβ compared to the original WT strain. These models represent suitable controls, or starting points, for studying the effect of transgenes or knock-in mutations on APP processing (Saito et al., Nat Neurosci 17:661-3, 2014). We introduced the early-onset familial Alzheimer’s disease (FAD) mutation M139T into the endogenous Rat Psen1 gene and provide an initial characterization of Aβ processing in this novel rat AD model.

Conclusion
The different humanized APP models (rat and mouse) expressing human Aβ and PSEN1 M139T are valuable controls to study APP processing in vivo allowing the use of a human Aβ ELISA which is more sensitive than the equivalent system for rodents. These animals will be made available to the research community.
Antibiotic-related gut dysbiosis induces lung immunodepression and worsens lung infection in mice
Authors: Dessein Rodrigue , Bauduin Marvin , Grandjean Teddy , Le Guern Rémi , Figeac Martin , Beury Delphine , Faure Karine , Faveeuw Christelle , Guery Benoit , Gosset Philippe , Kipnis Eric 
Published: October 2020

Abstract
Background
Gut dysbiosis due to the adverse effects of antibiotics affects outcomes of lung infection. Previous murine models relied on significant depletion of both gut and lung microbiota, rendering the analysis of immune gut-lung cross-talk difficult.
Here, we study the effects of antibiotic-induced gut dysbiosis without lung dysbiosis on lung immunity and the consequences on acute P. aeruginosa lung infection.

Methods
C57BL6 mice received 7 days oral vancomycin-colistin, followed by normal regimen or fecal microbial transplant or Fms-related tyrosine kinase 3 ligand (Flt3-Ligand) over 2 days, and then intra-nasal P. aeruginosa strain PAO1. Gut and lung microbiota were studied by next-generation sequencing, and lung infection outcomes were studied at 24 h. Effects of vancomycin-colistin on underlying immunity and bone marrow progenitors were studied in uninfected mice by flow cytometry in the lung, spleen, and bone marrow.

Results
Vancomycin-colistin administration induces widespread cellular immunosuppression in both the lung and spleen, decreases circulating hematopoietic cytokine Flt3-Ligand, and depresses dendritic cell bone marrow progenitors leading to worsening of P. aeruginosa lung infection outcomes (bacterial loads, lung injury, and survival). Reversal of these effects by fecal microbial transplant shows that these alterations are related to gut dysbiosis. Recombinant Flt3-Ligand reverses the effects of antibiotics on subsequent lung infection.

Conclusions
These results show that gut dysbiosis strongly impairs monocyte/dendritic progenitors and lung immunity, worsening outcomes of P. aeruginosa lung infection. Treatment with a fecal microbial transplant or immune stimulation by Flt3-Ligand both restore lung cellular responses to and outcomes of P. aeruginosa following antibiotic-induced gut dysbiosis.
Predicted functional interactome of Caenorhabditis elegans and a web tool for the functional interpretation of differentially expressed genes
Authors: Chen Peng-Cheng , Ruan Li , Jin Jie , Tao Yu-Tian , Ding Xiao-Bao , Zhang Hai-bo , Guo Wen-Ping , Yang Qiao-lei , Yao Heng , Chen Xin 
Published: October 2020

Abstract
Background
The nematode worm, Caenorhabditis elegans, is a saprophytic species that has been emerging as a standard model organism since the early 1960s. This species is useful in numerous fields, including developmental biology, neurobiology, and ageing. A high-quality comprehensive molecular interaction network is needed to facilitate molecular mechanism studies in C. elegans.

Results
We present the predicted functional interactome of Caenorhabditis elegans (FIC), which integrates functional association data from 10 public databases to infer functional gene interactions on diverse functional perspectives. In this work, FIC includes 108,550 putative functional associations with balanced sensitivity and specificity, which are expected to cover 21.42% of all C. elegans protein interactions, and 29.25% of these associations may represent protein interactions. Based on FIC, we developed a gene set linkage analysis (GSLA) web tool to interpret potential functional impacts from a set of differentially expressed genes observed in transcriptome analyses.

Conclusion
We present the predicted C. elegans interactome database FIC, which is a high-quality database of predicted functional interactions among genes. The functional interactions in FIC serve as a good reference interactome for GSLA to annotate differentially expressed genes for their potential functional impacts. In a case study, the FIC/GSLA system shows more comprehensive and concise annotations compared to other widely used gene set annotation tools, including PANTHER and DAVID. FIC and its associated GSLA are available at the website http://worm.biomedtzc.cn.
TREAT Early Arthralgia to Reverse or Limit Impending Exacerbation to Rheumatoid arthritis (TREAT EARLIER): a randomized, double-blind, placebo-controlled clinical trial protocol
Authors: Niemantsverdriet Ellis , Dakkak Yousra J. , Burgers Leonie E. , Bonte-Mineur Femke , Steup-Beekman Gerda M. , van der Kooij Sjoerd M. , Boom Hido D. , Allaart Cornelia F. , de Jong Pascal H. P. , van der Helm-van Mil Annette H. M. 
Published: October 2020

Abstract
Background
We present a study protocol for a randomized, double-blind, placebo-controlled trial that investigates the hypothesis if intervention in the symptomatic phase preceding clinical arthritis (clinically suspect arthralgia (CSA)) is effective in preventing progression from subclinical inflammation to clinically apparent persistent arthritis. Currently, rheumatoid arthritis (RA) can be recognized and diagnosed when arthritis (joint swelling) has become detectable at physical examination. Importantly, at this time, the immune processes have already matured, chronicity is established, and patients require long-standing treatment with disease-modifying anti-rheumatic drugs. The TREAT EARLIER trial studies the hypothesis that intervention in the symptomatic phase preceding clinical arthritis is more often successful in permanent disease modification because of less matured underlying disease processes.

Methods
A two-level definition to identify patients that are prone to develop RA is used. First, patients should have CSA and recent-onset arthralgia (< 1 year) that is suspect to progress to RA according to the expertise of the treating rheumatologist. Second, patients need to have subclinical inflammation of the hand or foot joints at 1.5 T MRI. The trial aims to recruit 230 participants from secondary care hospital settings across the south-west region of The Netherlands. Intervention will be randomly assigned and includes a single-dose of intramuscular 120 mg methylprednisolon followed by methotrexate (increasing dose to 25 mg/week orally) or placebo (both; injection and tablets) over the course of 1 year. Thereafter, participants are followed for another year. The primary endpoint is the development of clinically detectable arthritis, either fulfilling the 2010 criteria for RA or unclassified clinical arthritis of ≥ 2 joints, which persists for at least 2 weeks. DMARD-free status is a co-primary endpoint. The patient-reported outcomes functioning, along with workability and symptoms, are key secondary endpoints. Participants, caregivers (including those assessing the endpoints), and scientific staff are all blinded to the group assignment.

Discussion
This proof-of-concept study is the logical consequence of pre-work on the identification of patients with CSA with MRI-detected subclinical joint inflammation. It will test the hypothesis whether intervention in patients in this early phase with the cornerstone treatment of classified RA (methotrexate) hampers the development of persistent RA and reduce the disease burden of RA.

Trial registration
Dutch Trial Register NL4599 (NTR4853). Registered on 20 October 2014
Implementation of a stepped wedge cluster randomized trial to evaluate a hospital mobility program
Authors: Hastings Susan N. , Stechuchak Karen M. , Choate Ashley , Mahanna Elizabeth P. , Van Houtven Courtney , Allen Kelli D. , Wang Virginia , Sperber Nina , Zullig Leah , Bosworth Hayden B. , Coffman Cynthia J. 
Published: October 2020

Abstract
Background
Stepped wedge cluster randomized trials (SW-CRT) are increasingly used to evaluate new clinical programs, yet there is limited guidance on practical aspects of applying this design. We report our early experiences conducting a SW-CRT to examine an inpatient mobility program (STRIDE) in the Veterans Health Administration (VHA). We provide recommendations for future research using this design to evaluate clinical programs.

Methods
Based on data from study records and reflections from the investigator team, we describe and assess the design and initial stages of a SW-CRT, from site recruitment to program launch in 8 VHA hospitals.

Results
Site recruitment consisted of thirty 1-h conference calls with representatives from 22 individual VAs who expressed interest in implementing STRIDE. Of these, 8 hospitals were enrolled and randomly assigned in two stratified blocks (4 hospitals per block) to a STRIDE launch date. Block 1 randomization occurred in July 2017 with first STRIDE launch in December 2017; block 2 randomization occurred in April 2018 with first STRIDE launch in January 2019. The primary study outcome of discharge destination will be assessed using routinely collected data in the electronic health record (EHR). Within randomized blocks, two hospitals per sequence launched STRIDE approximately every 3 months with primary outcome assessment paused during the 3-month time period of program launch. All sites received 6–8 implementation support calls, according to a pre-specified schedule, from the time of recruitment to program launch, and all 8 sites successfully launched within their assigned 3-month window. Seven of the eight sites initially started with a limited roll out (for example on one ward) or modified version of STRIDE (for example, using existing staff to conduct walks until new positions were filled).

Conclusions
Future studies should incorporate sufficient time for site recruitment and carefully consider the following to inform design of SW-CRTs to evaluate rollout of a new clinical program: (1) whether a blocked randomization fits study needs, (2) the amount of time and implementation support sites will need to start their programs, and (3) whether clinical programs are likely to include a “ramp-up” period. Successful execution of SW-CRT designs requires both adherence to rigorous design principles and also careful consideration of logistical requirements for timing of program roll out.

Trial registration
ClinicalsTrials.gov NCT03300336. Prospectively registered on 3 October 2017.
Harnessing pongamia shell hydrolysate for triacylglycerol agglomeration by novel oleaginous yeast Rhodotorula pacifica INDKK
Authors: Kumar Kukkala Kiran , Deeba Farha , Sauraj  , Negi Yuvraj Singh , Gaur Naseem A. 
Published: October 2020

Abstract
Background
To meet the present transportation demands and solve food versus fuel issue, microbial lipid-derived biofuels are gaining attention worldwide. This study is focussed on high-throughput screening of oleaginous yeast by microwave-aided Nile red spectrofluorimetry and exploring pongamia shell hydrolysate (PSH) as a feedstock for lipid production using novel oleaginous yeast Rhodotorula pacifica INDKK.

Results
A new oleaginous yeast R. pacifica INDKK was identified and selected for microbial lipid production. R. pacifica INDKK produced maximum 12.8 ± 0.66 g/L of dry cell weight and 6.78 ± 0.4 g/L of lipid titre after 120 h of growth, showed high tolerance to pre-treatment-derived inhibitors such as 5-hydroxymethyl furfural (5-HMF), (2 g/L), furfural (0.5 g/L) and acetic acid (0.5 g/L), and ability to assimilate C3, C5 and C6 sugars. Interestingly, R. pacifica INDKK showed higher lipid accumulation when grown in alkali-treated saccharified PSH (AS-PSH) (0.058 ± 0.006 g/L/h) as compared to acid-treated detoxified PSH (AD-PSH) (0.037 ± 0.006 g/L/h) and YNB medium (0.055 ± 0.003 g/L/h). The major fatty acid constituents are oleic, palmitic, linoleic and linolenic acids with an estimated cetane number (CN) of about 56.7, indicating the good quality of fuel.

Conclusion
These results suggested that PSH and R. pacifica INDKK could be considered as potential feedstock for sustainable biodiesel production.
Association of TERT and DSP variants with microscopic polyangiitis and myeloperoxidase-ANCA positive vasculitis in a Japanese population: a genetic association study
Authors: Kawasaki Aya , Namba Natsumi , Sada Ken-ei , Hirano Fumio , Kobayashi Shigeto , Nagasaka Kenji , Sugihara Takahiko , Ono Nobuyuki , Fujimoto Takashi , Kusaoi Makio , Tamura Naoto , Yamagata Kunihiro , Sumida Takayuki , Hashimoto Hiroshi , Ozaki Shoichi , Makino Hirofumi , Arimura Yoshihiro , Harigai Masayoshi , Tsuchiya Naoyuki 
Published: October 2020

AbstractBackgroundInterstitial lung disease (ILD) is a severe complication with poor prognosis in anti-neutrophil cytoplasmic antibody (ANCA)-associated vasculitis (AAV). Prevalence of AAV-associated ILD (AAV-ILD) in Japan is considerably higher than that in Europe. Recently, we reported that aMUC5Bvariant rs35705950, the strongest susceptibility variant to idiopathic pulmonary fibrosis (IPF), was strikingly increased in AAV-ILD patients but not in AAV patients without ILD; however, due to the low allele frequency in the Japanese population, theMUC5Bvariant alone cannot account for the high prevalence of AAV-ILD in Japan. In this study, we examined whether other IPF susceptibility alleles inTERTandDSPgenes are associated with susceptibility to AAV subsets and AAV-ILD.MethodsFive hundred and forty-four Japanese patients with AAV and 5558 controls were analyzed. Among the AAV patients, 432 were positive for myeloperoxidase (MPO)-ANCA (MPO-AAV). A total of 176 MPO-AAV patients were positive and 216 were negative for ILD based on CT or high-resolution CT. Genotypes ofTERTandDSPvariants were determined by TaqMan SNP Genotyping Assay, and their association was tested by chi-square test.ResultsWhen the frequencies of the IPF risk allelesTERTrs2736100A andDSPrs2076295G were compared between AAV subsets and healthy controls, both alleles were significantly increased in microscopic polyangiitis (MPA) (TERT P = 2.3 × 10−4,Pc = 0.0023, odds ratio [OR] 1.38;DSP P = 6.9 × 10−4,Pc = 0.0069, OR 1.32) and MPO-AAV (TERT P = 1.5 × 10−4,Pc = 0.0015, OR 1.33;DSP P = 0.0011,Pc = 0.011, OR 1.26). On the other hand, no significant association was detected when the allele frequencies were compared between MPO-AAV patients with and without ILD.ConclusionsUnexpectedly,TERTandDSPIPF risk alleles were found to be associated with MPA and MPO-AAV, regardless of the presence of ILD. These findings suggest thatTERTandDSPmay be novel susceptibility genes to MPA/MPO-AAV and also that some susceptibility genes may be shared between IPF and MPA/MPO-AAV.
Epigenetic silencing of miR-342-3p in B cell lymphoma and its impact on autophagy
Authors: Zhang Min Yue , Calin George A. , Yuen Kit San , Jin Dong Yan , Chim Chor Sang 
Published: October 2020

Abstract
Background
miR-342-3p, localized to 14q32, is a tumor suppressor miRNA implicated in carcinogenesis. Given the presence of a promotor-associated CpG island for its host gene, EVL, we hypothesized that intronic miR-342-3p is a tumor suppressor co-regulated with host gene by promoter DNA methylation in B cell lymphoma.

Results
By bisulfite pyrosequencing-verified methylation-specific PCR (MSP), EVL/MIR342 methylation was detected in five (50%) lymphoma cell lines but not normal peripheral blood and tonsils. EVL/MIR342 methylation correlated with repression of both miR-342-3p and EVL in cell lines. In completely methylated SU-DHL-16 cells, 5-AzadC treatment resulted in promoter demethylation and re-expression of miR-342-3p and EVL. In 132 primary lymphoma samples, EVL/MIR342 was preferentially methylated in B cell lymphomas (N = 68; 68.7%) than T cell lymphoma (N = 8; 24.2%) by MSP (P < 0.0001). Moreover, EVL/MIR342 methylation was associated with lower miR-342-3p expression in 79 primary NHL (P = 0.0443). In SU-DHL-16 cells, the tumor suppressor function of miR-342-3p was demonstrated by the inhibition of cellular proliferation and increase of cell death upon over-expression of miR-342-3p. Mechanistically, overexpression of miR-342-3p resulted in a decrease of LC3-II, a biomarker of autophagy, which was pro-survival for SU-DHL-16. Pre-treatment with 3-methyladenine, an autophagy inhibitor, abrogated tumor suppression associated with miR-342-3p overexpression. By luciferase assay, MAP1LC3B, a precursor of LC3-II, was confirmed as a direct target of miR-342-3p. Finally, in SU-DHL-16 cells, overexpression of miR-342-3p downregulated the known target DNMT1, with promoter demethylation and re-expression of tumor suppressor E-cadherin.

Conclusions
Intronic miR-342-3p is co-regulated with its host gene EVL by tumor-specific promoter DNA methylation in B cell lymphoma. The tumor suppressor function of miR-342-3p was mediated via inhibition of pro-survival autophagy by targeting MAP1LC3B and downregulation of DNMT1 with demethylation and re-expression of tumor suppressor genes.