bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genome-wide transcriptome profiling of human trabecular meshwork cells treated with TGF-β2
Authors: Callaghan Breedge , Lester Karen , Lane Brian , Fan Xiaochen , Goljanek-Whysall Katarzyna , Simpson David A. , Sheridan Carl , Willoughby Colin E. 
Published: June 2022

AbstractGlaucoma is a complex neurodegenerative disease resulting in progressive optic neuropathy and is a leading cause of irreversible blindness worldwide. Primary open angle glaucoma (POAG) is the predominant form affecting 65.5 million people globally. Despite the prevalence of POAG and the identification of over 120 glaucoma related genetic loci, the underlaying molecular mechanisms are still poorly understood. The transforming growth factor beta (TGF-β) signalling pathway is implicated in the molecular pathology of POAG. To gain a better understanding of the role TGF-β2 plays in the glaucomatous changes to the molecular pathology in the trabecular meshwork, we employed RNA-Seq to delineate the TGF-β2 induced changes in the transcriptome of normal primary human trabecular meshwork cells (HTM). We identified a significant number of differentially expressed genes and associated pathways that contribute to the pathogenesis of POAG. The differentially expressed genes were predominantly enriched in ECM regulation, TGF-β signalling, proliferation/apoptosis, inflammation/wound healing, MAPK signalling, oxidative stress and RHO signalling. Canonical pathway analysis confirmed the enrichment of RhoA signalling, inflammatory-related processes, ECM and cytoskeletal organisation in HTM cells in response to TGF-β2. We also identified novel genes and pathways that were affected after TGF-β2 treatment in the HTM, suggesting additional pathways are activated, including Nrf2, PI3K-Akt, MAPK and HIPPO signalling pathways. The identification and characterisation of TGF-β2 dependent differentially expressed genes and pathways in HTM cells is essential to understand the patho-physiology of glaucoma and to develop new therapeutic agents.
TACSTD2 upregulation is an early reaction to lung infection
Authors: Lenárt Sára , Lenárt Peter , Knopfová Lucia , Kotasová Hana , Pelková Vendula , Sedláková Veronika , Vacek Ondřej , Pokludová Jana , Čan Vladimír , Šmarda Jan , Souček Karel , Hampl Aleš , Beneš Petr 
Published: June 2022

AbstractTACSTD2encodes a transmembrane glycoprotein Trop2 commonly overexpressed in carcinomas. While the Trop2 protein was discovered already in 1981 and first antibody–drug conjugate targeting Trop2 were recently approved for cancer therapy, the physiological role of Trop2 is still not fully understood. In this article, we show thatTACSTD2/Trop2 expression is evolutionarily conserved in lungs of various vertebrates. By analysis of publicly available transcriptomic data we demonstrate thatTACSTD2level consistently increases in lungs infected with miscellaneous, but mainly viral pathogens. Single cell and subpopulation based transcriptomic data revealed that the major source ofTACSTD2transcript are lung epithelial cells and their progenitors and thatTACSTD2is induced directly in lung epithelial cells following infection. Increase inTACSTD2expression may represent a mechanism to maintain/restore epithelial barrier function and contribute to regeneration process in infected/damaged lungs.
Telomere-to-telomere human DNA replication timing profiles
Authors: Massey Dashiell J. , Koren Amnon 
Published: June 2022

AbstractThe spatiotemporal organization of DNA replication produces a highly robust and reproducible replication timing profile. Sequencing-based methods for assaying replication timing genome-wide have become commonplace, but regions of high repeat content in the human genome have remained refractory to analysis. Here, we report the first nearly-gapless telomere-to-telomere replication timing profiles in human, using the T2T-CHM13 genome assembly and sequencing data for five cell lines. We find that replication timing can be successfully assayed in centromeres and large blocks of heterochromatin. Centromeric regions replicate in mid-to-late S-phase and contain replication-timing peaks at a similar density to other genomic regions, while distinct families of heterochromatic satellite DNA differ in their bias for replicating in late S-phase. The high degree of consistency in centromeric replication timing across chromosomes within each cell line prompts further investigation into the mechanisms dictating that some cell lines replicate their centromeres earlier than others, and what the consequences of this variation are.
HideRNAs protect against CRISPR-Cas9 re-cutting after successful single base-pair gene editing
Authors: Harmsen Tim J. W. , Pritchard Colin E. J. , Riepsaame Joey , van de Vrugt Henri J. , Huijbers Ivo J. , te Riele Hein 
Published: June 2022

AbstractPromiscuous activity of the Streptococcus pyogenes DNA nuclease CRISPR-Cas9 can result in destruction of a successfully modified sequence obtained by templated repair of a Cas9-induced DNA double-strand break. To avoid re-cutting, additional target-site-disruptions (TSDs) are often introduced on top of the desired base-pair alteration in order to suppress target recognition. These TSDs may lower the efficiency of introducing the intended mutation and can cause unexpected phenotypes. Alternatively, successfully edited sites can be protected against Cas9 re-cutting activity. This method exploits the finding that Cas9 complexed to trimmed guideRNAs can still tightly bind specific genomic sequences but lacks nuclease activity. We show here that the presence of a guideRNA plus a trimmed guideRNA that matches the successfully mutated sequence, which we call hideRNA, can enhance the recovery of precise single base-pair substitution events tenfold. The benefit of hideRNAs in generating a single point mutation was demonstrated in cell lines using plasmid-based delivery of CRISPR-Cas9 components and in mouse zygotes injected with Cas9/guideRNA plus Cas9/hideRNA ribonucleoprotein complexes. However, hRNA protection sometimes failed, which likely reflects an unfavorable affinity of hRNA/Cas9 versus gRNA/Cas9 for the DNA target site. HideRNAs can easily be implemented into current gene editing protocols and facilitate the recovery of single base-pair substitution. As such, hideRNAs are of great value in gene editing experiments demanding high accuracy.
A method for the controllable fabrication of optical fiber-based localized surface plasmon resonance sensors
Authors: Calatayud-Sanchez Alba , Ortega-Gomez Angel , Barroso Javier , Zubia Joseba , Benito-Lopez Fernando , Villatoro Joel , Basabe-Desmonts Lourdes 
Published: June 2022

AbstractOptical fiber-based Localized Surface Plasmon Resonance (OF-LSPR) biosensors have emerged as an ultra-sensitive miniaturized tool for a great variety of applications. Their fabrication by the chemical immobilization of gold nanoparticles (AuNPs) on the optic fiber end face is a simple and versatile method. However, it can render poor reproducibility given the number of parameters that influence the binding of the AuNPs. In order to develop a method to obtain OF-LSPR sensors with high reproducibility, we studied the effect that factors such as temperature, AuNPs concentration, fiber core size and time of immersion had on the number and aggregation of AuNPs on the surface of the fibers and their resonance signal. Our method consisted in controlling the deposition of a determined AuNPs density on the tip of the fiber by measuring its LSPR signal (or plasmonic signal, Sp) in real-time. Sensors created thus were used to measure changes in the refractive index of their surroundings and the results showed that, as the number of AuNPs on the probes increased, the changes in the Sp maximum values were ever lower but the wavelength shifts were higher. These results highlighted the relevance of controlling the relationship between the sensor composition and its performance.
Use and subjective experience of the impact of motor-assisted movement exercisers in people with amyotrophic lateral sclerosis: a multicenter observational study
Authors: Maier André , Gaudlitz Marcel , Grehl Torsten , Weyen Ute , Steinbach Robert , Grosskreutz Julian , Rödiger Annekathrin , Koch Jan Christoph , Lengenfeld Teresa , Weydt Patrick , Günther René , Wolf Joachim , Baum Petra , Metelmann Moritz , Dorst Johannes , Ludolph Albert C. , Kettemann Dagmar , Norden Jenny , Koc Ruhan Yasemin , Walter Bertram , Hildebrandt Barbara , Münch Christoph , Meyer Thomas , Spittel Susanne 
Published: June 2022

AbstractMotor-assisted movement exercisers (MME) are devices that assist with physical therapy in domestic settings for people living with ALS. This observational cross-sectional study assesses the subjective experience of the therapy and analyzes users' likelihood of recommending treatment with MME. The study was implemented in ten ALS centers between February 2019 and October 2020, and was coordinated by the research platform Ambulanzpartner. Participants assessed symptom severity, documented frequency of MME use and rated the subjective benefits of therapy on a numerical scale (NRS, 0 to 10 points, with 10 being the highest). The Net Promotor Score (NPS) determined the likelihood of a participant recommending MME. Data for 144 participants were analyzed. Weekly MME use ranged from 1 to 4 times for 41% of participants, 5 to 7 times for 42%, and over 7 times for 17%. Particularly positive results were recorded in the following domains: amplification of a sense of achievement (67%), diminution of the feeling of having rigid limbs (63%), diminution of the feeling of being immobile (61%), improvement of general wellbeing (55%) and reduction of muscle stiffness (52%). Participants with more pronounced self-reported muscle weakness were more likely to note a beneficial effect on the preservation and improvement of muscle strength during MME treatment (p < 0.05). Overall, the NPS for MME was high (+ 61). High-frequency MME-assisted treatment (defined as a minimum of five sessions a week) was administered in the majority of participants (59%) in addition to physical therapy. Most patients reported having achieved their individual therapeutic objectives, as evidenced by a high level of satisfaction with MME therapy. The results bolster the justification for extended MME treatment as part of a holistic approach to ALS care.
A mechano-sensing mechanism for waving in plant roots
Authors: Zhang Zhenwei , van Ophem Danie , Chelakkot Raghunath , Lazarovitch Naftali , Regev Ido 
Published: June 2022

AbstractArabidopsis roots grown on inclined agar surfaces exhibit unusual sinusoidal patterns known as root-waving. The origin of these patterns has been ascribed to both genetic and environmental factors. Here we propose a mechano-sensing model for root-waving, based on a combination of friction induced by gravitropism, the elasticity of the root and the anchoring of the root to the agar by thin hairs, and demonstrate its relevance to previously obtained experimental results. We further test the applicability of this model by performing experiments in which we measure the effect of gradually changing the inclination angles of the agar surfaces on the wavelength and other properties of the growing roots. We find that the observed dynamics is different than the dynamics reported in previous works, but that it can still be explained using the same mechano-sensing considerations. This is supported by the fact that a scaling relation derived from the model describes the observed dependence of the wavelength on the tilt angle for a large range of angles. We also compare the prevalence of waving in different plant species and show that it depends on root thickness as predicted by the model. The results indicate that waving can be explained using mechanics and gravitropism alone and that mechanics may play a greater role in root growth and form than was previously considered.
Experimental analysis of liquid metal galinstan for electronics actuation
Authors: Anwar M.S. , Ehlers F. , Bangert A. 
Published: June 2022

AbstractThe experimental interfacial tension measurements of galinstan as a function of applied DC voltages are presented. The measurements are based on a tailored, modified pendent drop setup to make it suitable for this experiment. The findings rationalise Galinstan corresponding to Marangoni flow that actuates under the influence of a change in interfacial tension, resulting from applied voltages. Galinstan is substantiated as an actuation medium to enable ON or OFF states by using a very low applied voltage (∼ 0.8V). The illustrated nature of measurements performed in this work has significance for a variety of reconfigurable RF applications, by enabling well‐controlled actuations.
Comparison of patient tolerance and acceptability of magnet-controlled capsule endoscopy and flexible endoscopy in the investigation of dyspepsia
Authors: Tai Foong Way David , Ching Hey Long , Sloan Marion , Sidhu Reena , McAlindon Mark 
Published: June 2022

Abstract
Background and study aims Oropharyngeal intubation during Esophagogastroduodenoscopy (EGD) is uncomfortable, associated with aerosol generation and transmission of airborne microbes. Less-invasive alternatives may be better tolerated. In this study, patient tolerance and acceptability of EGD and transnasal endoscopy (TNE) have been compared with magnet-controlled capsule endoscopy (MACE).
Patients and methods A comparison of MACE with EGD and TNE in the investigation of dyspepsia was performed. Factors affecting patient tolerance and acceptability were examined using the Endoscopy Concerns Scale (ECS) and Universal Patient Centeredness Questionnaire (UPC-Q).
Results Patients were significantly more distressed (scoring least to most distress: 1–10) by gagging (6 vs 1), choking (5 vs 1), bloating (2 vs 1), instrumentation (4 vs 1), discomfort during (5 vs 1) and after (2 vs 1) EGD compared to MACE (all P < 0.0001). Patients were more distressed by instrumentation (5 vs 1) and discomfort during (5 vs 1) TNE compared to MACE (P = 0.001). Patients were more accepting of MACE than EGD and TNE with a UPC-Q score (scoring least to most acceptable: 0–100) lower for EGD (50 vs 98, P < 0.0001) and TNE (75 vs 88, P = 0.007) than MACE, and a post-procedure ECS score (scoring most to least acceptable: 10–100) higher for EGD (34 vs 11, P < 0.0001) and TNE (25 vs 10.5, P = 0.001) than MACE. MACE would be preferred by 83 % and 64 % of patients even if EGD or TNE respectively was subsequently recommended to obtain biopsies in half of examinations.
Conclusions Gagging and choking during instrumentation, the main causes of patient distress during EGD, occurred less during TNE but tolerance, acceptability and patient experience favored MACE.
Prospective multicenter study of the efficacy and safety of cold forceps polypectomy for ≤ 6-mm non-ampullary duodenal low-grade adenomas
Authors: Kanzaki Hiromitsu , Horii Joichiro , Takenaka Ryuta , Nakagawa Hiroyuki , Matsueda Kazuhiro , Tsuzuki Takao , Kita Masahide , Yamasaki Yasushi , Tanaka Takehiro , Iwamuro Masaya , Kawano Seiji , Kawahara Yoshiro , Tomoda Jun , Okada Hiroyuki 
Published: June 2022

Abstract
Background and study aims Because the endoscopic treatment for non-ampullary duodenal adenoma (NADA) has a non-negligible risk of adverse events (AEs), a safe and easy treatment for NADA is desirable. This was a multicenter prospective trial evaluating the efficacy and safety of cold forceps polypectomy (CFP) for diminutive NADAs.
Patients and methods This study was prospectively conducted at six general hospitals and one university hospital. The inclusion criteria were histologic and endoscopic diagnosis of low-grade NADA measuring ≤ 6 mm. A second endoscopy was scheduled for 1 month after CFP. After confirmation of the success of CFP, 6-month and 12-month surveillance endoscopies were scheduled. The primary endpoint was the endoscopic and histologic disease disappearance rates at the 12-month endoscopy.
Results Thirty-nine lesions from 38 patients were prospectively included. Median tumor size at enrollment was 5 mm (range 3–6 mm). There were four cases of remnant lesions at the second endoscopy, and the lesion disappearance rate of single CFP was 89.7 % (35 /39; 95 % confidence interval (CI), 76.9 %–97.9 %). In three cases, complete removal of the lesion was achieved with a single re-CFP, but one case required four repeat CFPs. The lesion disappearance rate at 12-month endoscopy was 97.4 % (38 /39; 95 %CI, 86.8 %–99.5 %). During the follow-up period, no AEs related to CFP were observed.
Conclusions CFP for NADA ≤ 6 mm was safe and effective in this study. This common endoscopic method to remove lesions may be an option for treatment of diminutive NADAs.
Efficacy and safety of endoscopic duodenal stent versus endoscopic or surgical gastrojejunostomy to treat malignant gastric outlet obstruction: systematic review and meta-analysis
Authors: Krishnamoorthi Rajesh , Bomman Shivanand , Benias Petros , Kozarek Richard A. , Peetermans Joyce A. , McMullen Edmund , Gjata Ornela , Irani Shayan S. 
Published: June 2022

Abstract
Background and study aims Malignant disease accounts for up to 80 % of gastric outlet obstruction (GOO) cases, which may be treated with duodenal self-expanding metal stents (SEMS), surgical gastrojejunostomy (GJ), and more recently endoscopic-ultrasound-guided gastroenterostomy (EUS-GE). These three treatments have not been compared head-to-head in a randomized trial.
Methods We searched the Embase and MEDLINE databases for studies published January 2015−February 2021 assessing treatment of malignant GOO using duodenal SEMS, endoscopic (EUS-GE) or surgical (laparoscopic or open) GJ. Efficacy outcomes assessed included technical and clinical success rates, GOO recurrence and reintervention. Safety outcomes included procedure-related bleeding or perforation, and stent-related events for the duodenal SEMS and EUS-GE arms.
Results EUS-GE had a lower rate of technical success (95.3%) than duodenal SEMS (99.4 %) or surgical GJ (99.9%) (P = 0.0048). For duodenal SEMS vs. EUS-GE vs. surgical GJ, rates of clinical success (88.9 % vs. 89.0 % vs. 92.3 % respectively, P = 0.49) were similar. EUS-GE had a lower rate of GOO recurrence based on limited data (P = 0.0036), while duodenal SEMS had a higher rate of reintervention (P = 0.041). Overall procedural complications were similar (duodenal SEMS 18.7 % vs. EUS-GE 21.9 % vs. surgical GJ 23.8 %, P = 0.32), but estimated bleeding rate was lowest (P = 0.0048) and stent occlusion rate was highest (P = 0.0002) for duodenal SEMS.
Conclusions Duodenal SEMS, EUS-GE, and surgical GJ showed similar clinical efficacy for the treatment of malignant GOO. Duodenal SEMS had a lower procedure-related bleeding rate but higher rate of reintervention.
Role of gastric per-oral endoscopic myotomy (G-POEM) in post-lung transplant patients: a multicenter experience
Authors: Ichkhanian Yervant , Hwang Joo Ha , Ofosu Andrew , Li Andrew A , Szvarca Daniel , Draganov Peter V. , Yang Dennis , Alsheik Eva , Zuchelli Tobias , Piraka Cyrus , Mony Shruti , Khashab Mouen A. 
Published: June 2022

Abstract
Background and study aims Gastroparesis post-lung transplant (LTx) can lead to increased risk of gastroesophageal reflux (GER) and accelerated graft dysfunction. We aimed to evaluate the efficacy and safety of gastric per-oral endoscopic myotomy (G-POEM), a promising tool in patients with refractory gastroparesis, for managing refractory gastroparesis and GER in post-LTx patients.
Patents and methods This was a multicenter retrospective study on post-LTx patients who underwent G-POEM for management of gastroparesis and GER that were refractory to standard medical therapy. The primary outcome was clinical success post-G-POEM. Secondary outcomes included the rate of post-G-POEM objective esophageal pH exam normalization, rate of gastric emptying scintigraphy (GES) normalization, technical success, and adverse events.
Results A total of 20 patients (mean age 54.7 ± 14.1 years, Female 50 %) underwent G-POEM at a median time of 13 months (interquartile range 6.5–13.5) post-LTx. All G-POEM procedures were technically successful. Clinical success was achieved in 17 (85 %) patients during a median follow-up time of 8.9 (IQR: 3–17) months post-G-POEM. Overall GCSI and two of its subscales (bloating and postprandial fullness/early satiety) improved significantly following G-POEM. Two patients (10 %) developed post-procedural AEs (delayed bleeding 1, pyloric stenosis 1, both moderate in severity). Post-G-POEM GES improvement was achieved in 12 of 16 patients (75 %). All 20 patients were on proton pump inhibitors pre-G-POEM, as opposed to five post-G-POEM. Post-G-POEM PH study normalization was noted in nine of 10 patients (90 %) who underwent both pre- and post-G-poem pH testing.
Conclusions G-POEM is a promising noninvasive therapeutic tool for management of refractory gastroparesis and GER post-LTx.
Rettungsdienstlich betreute außerklinische Geburten – seltenes Ereignis und Herausforderung zugleich: eine retrospektive Analyse über 5 Jahre in Hamburg
Authors: Hensel Mario , Mallon Anastasia , Paschen Hans-Richard , Tank Sascha , Wenderoth Stephan , Kerner Thoralf 
Published: June 2022

Zusammenfassung
Hintergrund Analyse rettungsdienstlich betreuter Geburten in
Hamburg über einen 5-Jahres-Zeitraum.
Methodik Retrospektive Untersuchung aller außerklinischen
Geburten von 2007 bis 2011.
Ergebnisse Insgesamt wurden im Untersuchungszeitraum 103 Kinder
präklinisch geboren, die postnatal gemeinsam mit der Mutter in eine Klinik eingeliefert
wurden. Das entsprach 0,1% aller Geburten und 0,01% aller Rettungsdiensteinsätze. Es gab keine
mütterlichen und kindlichen Todesfälle ≤ 7 Tage postnatal. Ein Neugeborenes (40. SSW) starb 8
Tage postnatal an einer Lungenfehlbildung. Von den Neugeborenen wiesen 24% eine Hypothermie
< 35 °C und 4% eine Hypoglykämie auf. Mütterliche Verletzungen traten seltener auf, wenn
eine Hebamme anwesend war.
Schlussfolgerungen Relevante praktische Erfahrungen können von
Rettungsdienstmitarbeitern aufgrund der Seltenheit präklinischer Geburten nicht erlangt
werden. Dieses Defizit muss durch adäquate Aus- und Fortbildungsmaßnahmen ausgeglichen
werden.
Energy harvesting by piezo-tires and their life cycle assessment
Authors: Hazeri Somayyeh , Mulligan Catherine N. 
Published: June 2022

Piezoelectric materials can convert mechanical energy into electrical energy. These materials have the potential to provide reliable and cost-effective replacements of energy sources. It can ultimately have the potential to reduce fuel costs in vehicles. The use of piezoelectric materials in pneumatic tires enables capturing the waste energy of cars because of deformations in tires. An experimental setup was designed and constructed to simulate the movement and pressure inside the tire of a car. Piezoelectric elements were attached to the external perimeter of the model tire. Based on the experimental results, this method produced 2.31 W for 56 piezo-elements comparable to 2.3 W for 160 piezo-elements found in the literature. The results showed that placing piezoelectric elements on the outer surface of tires has a higher potential in harvesting the waste energy in vehicle tires. The harvested energy has a direct relation with the compressive stress under the contact patch of the tire. In addition, the harvested energy increases by increasing the velocity and applied weight. In addition to the experimental study, the environmental effects of harvesting waste mechanical energy in tires by using piezoelectric materials bonded to tires were evaluated through a life cycle assessment. The results showed that in addition to harvesting some of the waste energy in cars, it contributes a slightly higher environmental load than ordinary tires. Further evaluation of the technology is required to measure the durability and the lifetime of piezoelectric materials.