bluuebunny/crossref_metadata_2025_split huggingface dataset:
A small RNA regulates pprM, a modulator of pleiotropic proteins promoting DNA repair, in Deinococcus radiodurans under ionizing radiation
Authors: Villa Jordan K. , Han Runhua , Tsai Chen-Hsun , Chen Angela , Sweet Philip , Franco Gabriela , Vaezian Respina , Tkavc Rok , Daly Michael J. , Contreras Lydia M. 
Published: June 2021

AbstractNetworks of transcriptional and post-transcriptional regulators are critical for bacterial survival and adaptation to environmental stressors. While transcriptional regulators provide rapid activation and/or repression of a wide-network of genes, post-transcriptional regulators, such as small RNAs (sRNAs), are also important to fine-tune gene expression. However, the mechanisms of sRNAs remain poorly understood, especially in less-studied bacteria. Deinococcus radiodurans is a gram-positive bacterium resistant to extreme levels of ionizing radiation (IR). Although multiple unique regulatory systems (e.g., the Radiation and Desiccation Response (RDR)) have been identified in this organism, the role of post-transcriptional regulators has not been characterized within the IR response. In this study, we have characterized an sRNA, PprS (formerly Dsr2), as a post-transcriptional coordinator of IR recovery in D. radiodurans. PprS showed differential expression specifically under IR and knockdown of PprS resulted in reduced survival and growth under IR, suggesting its importance in regulating post-radiation recovery. We determined a number of potential RNA targets involved in several pathways including translation and DNA repair. Specifically, we confirmed that PprS binds within the coding region to stabilize the pprM (DR_0907) transcript, a RDR modulator. Overall, these results are the first to present an additional layer of sRNA-based control in DNA repair pathways associated with bacterial radioresistance.
Distinct effects of heterogeneity and noise on gamma oscillation in a model of neuronal network with different reversal potential
Authors: Zheng Tianyi , Kotani Kiyoshi , Jimbo Yasuhiko 
Published: June 2021

AbstractGamma oscillation is crucial in brain functions such as attentional selection, and is inextricably linked to both heterogeneity and noise (or so-called stochastic fluctuation) in neuronal networks. However, under coexistence of these factors, it has not been clarified how the synaptic reversal potential modulates the entraining of gamma oscillation. Here we show distinct effects of heterogeneity and noise in a population of modified theta neurons randomly coupled via GABAergic synapses. By introducing the Fokker-Planck equation and circular cumulants, we derive a set of two-cumulant macroscopic equations. In bifurcation analyses, we find a stabilizing effect of heterogeneity and a nontrivial effect of noise that results in promoting, diminishing, and shifting the oscillatory region, and is largely dependent on the reversal potential of GABAergic synapses. These findings are verified by numerical simulations of a finite-size neuronal network. Our results reveal that slight changes in reversal potential and magnitude of stochastic fluctuations can lead to immediate control of gamma oscillation, which would results in complex spatio-temporal dynamics for attentional selection and recognition.
High-resolution transcriptional landscape of xeno-free human induced pluripotent stem cell-derived cerebellar organoids
Authors: Nayler Samuel , Agarwal Devika , Curion Fabiola , Bowden Rory , Becker Esther B. E. 
Published: June 2021

AbstractCurrent protocols for producing cerebellar neurons from human pluripotent stem cells (hPSCs) often rely on animal co-culture and mostly exist as monolayers, limiting their capability to recapitulate the complex processes in the developing cerebellum. Here, we employed a robust method, without the need for mouse co-culture to generate three-dimensional cerebellar organoids from hPSCs that display hallmarks of in vivo cerebellar development. Single-cell profiling followed by comparison to human and mouse cerebellar atlases revealed the presence and maturity of transcriptionally distinct populations encompassing major cerebellar cell types. Encapsulation with Matrigel aimed to provide more physiologically-relevant conditions through recapitulation of basement-membrane signalling, influenced both growth dynamics and cellular composition of the organoids, altering developmentally relevant gene expression programmes. We identified enrichment of cerebellar disease genes in distinct cell populations in the hPSC-derived cerebellar organoids. These findings ascertain xeno-free human cerebellar organoids as a unique model to gain insight into cerebellar development and its associated disorders.
Selective stimulation of the ferret abdominal vagus nerve with multi-contact nerve cuff electrodes
Authors: Shulgach Jonathan A. , Beam Dylan W. , Nanivadekar Ameya C. , Miller Derek M. , Fulton Stephanie , Sciullo Michael , Ogren John , Wong Liane , McLaughlin Bryan L. , Yates Bill J. , Horn Charles C. , Fisher Lee E. 
Published: June 2021

AbstractDysfunction and diseases of the gastrointestinal (GI) tract are a major driver of medical care. The vagus nerve innervates and controls multiple organs of the GI tract and vagus nerve stimulation (VNS) could provide a means for affecting GI function and treating disease. However, the vagus nerve also innervates many other organs throughout the body, and off-target effects of VNS could cause major side effects such as changes in blood pressure. In this study, we aimed to achieve selective stimulation of populations of vagal afferents using a multi-contact cuff electrode wrapped around the abdominal trunks of the vagus nerve. Four-contact nerve cuff electrodes were implanted around the dorsal (N = 3) or ventral (N = 3) abdominal vagus nerve in six ferrets, and the response to stimulation was measured via a 32-channel microelectrode array (MEA) inserted into the left or right nodose ganglion. Selectivity was characterized by the ability to evoke responses in MEA channels through one bipolar pair of cuff contacts but not through the other bipolar pair. We demonstrated that it was possible to selectively activate subpopulations of vagal neurons using abdominal VNS. Additionally, we quantified the conduction velocity of evoked responses to determine what types of nerve fibers (i.e., Aδ vs. C) responded to stimulation. We also quantified the spatial organization of evoked responses in the nodose MEA to determine if there is somatotopic organization of the neurons in that ganglion. Finally, we demonstrated in a separate set of three ferrets that stimulation of the abdominal vagus via a four-contact cuff could selectively alter gastric myoelectric activity, suggesting that abdominal VNS can potentially be used to control GI function.
Canopy distribution and microclimate preferences of sterile and wild Queensland fruit flies
Authors: Inskeep Jess R. , Allen Andrew P. , Taylor Phillip W. , Rempoulakis Polychronis , Weldon Christopher W. 
Published: June 2021

AbstractInsects tend to live within well-defined habitats, and at smaller scales can have distinct microhabitat preferences. These preferences are important, but often overlooked, in applications of the sterile insect technique. Different microhabitat preferences of sterile and wild insects may reflect differences in environmental tolerance and may lead to spatial separation in the field, both of which may reduce the control program efficiency. In this study, we compared the diurnal microhabitat distributions of mass-reared (fertile and sterile) and wild Queensland fruit flies, Bactrocera tryoni (Froggatt) (Diptera: Tephritidae). Flies were individually tagged and released into field cages containing citrus trees. We recorded their locations in the canopies (height from ground, distance from canopy center), behavior (resting, grooming, walking, feeding), and the abiotic conditions on occupied leaves (temperature, humidity, light intensity) throughout the day. Flies from all groups moved lower in the canopy when temperature and light intensity were high, and humidity was low; lower canopy regions provided shelter from these conditions. Fertile and sterile mass-reared flies of both sexes were generally lower in the canopies than wild flies. Flies generally fed from the top sides of leaves that were lower in the canopy, suggesting food sources in these locations. Our observations suggest that mass-reared and wild B. tryoni occupy different locations in tree canopies, which could indicate different tolerances to environmental extremes and may result in spatial separation of sterile and wild flies when assessed at a landscape scale.
Few-qubit quantum refrigerator for cooling a multi-qubit system
Authors: Arısoy Onat , Müstecaplıoğlu Özgür E. 
Published: June 2021

AbstractWe propose to use a few-qubit system as a compact quantum refrigerator for cooling an interacting multi-qubit system. We specifically consider a central qubit coupled to N ancilla qubits in a so-called spin-star model to be used as refrigerant by means of short interactions with a many-qubit system to be cooled. We first show that if the interaction between the qubits is of the longitudinal and ferromagnetic Ising model form, the central qubit is colder than the environment. We summarize how preparing the refrigerant qubits using the spin-star model paves the way for the cooling of a many-qubit system by means of a collisional route to thermalization. We discuss a simple refrigeration cycle, considering the operation cost and cooling efficiency, which can be controlled by N and the qubit–qubit interaction strength. Besides, bounds on the achievable temperature are established. Such few-qubit compact quantum refrigerators can be significant to reduce dimensions of quantum technology applications, can be easy to integrate into all-qubit systems, and can increase the speed and power of quantum computing and thermal devices.
Creation of quantum entangled states of Rydberg atoms via chirped adiabatic passage
Authors: Pachniak Elliot , Malinovskaya Svetlana A. 
Published: June 2021

AbstractEntangled states are crucial for modern quantum enabled technology which makes their creation key for future developments. In this paper, a robust quantum control methodology is presented to create entangled states of two typical classes, the W and the Greenberger–Horne–Zeilinger (GHZ). It was developed from the analysis of a chain of alkali atoms $$^{87}Rb$$

87

R
b

interaction with laser pulses, which leads to the two-photon transitions from the ground to the Rydberg states with a predetermined magnetic quantum number. The methodology is based on the mechanism of the two-photon excitation, adiabatic for the GHZ and non-adiabatic for the W state, induced by the overlapping chirped pulses and governed by the Rabi frequency, the one-photon detuning, and the strength of the Rydberg–Rydberg interactions.
A genome-wide CRISPR/Cas9 screen to identify phagocytosis modulators in monocytic THP-1 cells
Authors: Lindner Benjamin , Martin Eva , Steininger Monika , Bundalo Aleksandra , Lenter Martin , Zuber Johannes , Schuler Michael 
Published: June 2021

AbstractPhagocytosis of microbial pathogens, dying or dead cells, and cell debris is essential to maintain tissue homeostasis. Impairment of these processes is associated with autoimmunity, developmental defects and toxic protein accumulation. However, the underlying molecular mechanisms of phagocytosis remain incompletely understood. Here, we performed a genome-wide CRISPR knockout screen to systematically identify regulators involved in phagocytosis ofStaphylococcus(S.)aureusby human monocytic THP-1 cells. The screen identified 75 hits including known regulators of phagocytosis, e.g. members of the actin cytoskeleton regulation Arp2/3 and WAVE complexes, as well as genes previously not associated with phagocytosis. These novel genes are involved in translational control (EIF5A and DHPS) and the UDP glycosylation pathway (SLC35A2, SLC35A3, UGCG and UXS1) and were further validated by single gene knockout experiments. Whereas the knockout of EIF5A and DHPS impaired phagocytosis, knocking out SLC35A2, SLC35A3, UGCG and UXS1 resulted in increased phagocytosis. In addition toS. aureusphagocytosis, the above described genes also modulate phagocytosis ofEscherichia coliand yeast-derived zymosan A. In summary, we identified both known and unknown genetic regulators of phagocytosis, the latter providing a valuable resource for future studies dissecting the underlying molecular and cellular mechanisms and their role in human disease.
Newly diagnosed diabetes has high risk for cardiovascular outcome in ischemic stroke patients
Authors: Cho Kyung-Hee , Kwon Sun U. , Lee Ji Sung , Yu Sungwook , Cho A-Hyun 
Published: June 2021

AbstractWe investigated cardiovascular outcomes in ischemic stroke patients with newly diagnosed diabetes mellitus (DM) compared with those of patients with previously known DM and no DM using the glycosylated hemoglobin (HbA1c) criteria. The relationship between new DM diagnosis and cardiovascular risk remains unclear to date. We performed post hoc analysis using the data of participants from the Prevention of Cardiovascular events in iSchemic Stroke patients with high risk of cerebral hemOrrhage (PICASSO) trial. Newly diagnosed DM was defined as HbA1c of ≥ 6.5% without known DM history. The outcome was the incidence of composite cardiovascular events, including stroke (ischemic and hemorrhagic), myocardial infarction, and cardiovascular death. In total, 1306 patients were included; 38 patients (2.9%) had newly diagnosed DM; 438 patients (33.5%), known DM; and 830 patients (63.6%), no DM. In patients with newly diagnosed DM, known DM, and no DM, the incidence of ischemic stroke was 8.93, 3.79, and 2.64 per 100 person-years (log-rank test; p = 0.0092), while that of composite cardiovascular events was 8.93, 5.92, and 3.87 per 100 person-years (p = 0.025), respectively. Newly diagnosed DM was an important risk factor for ischemic stroke and composite cardiovascular events after ischemic stroke.Registration: URL: https://www.clinicaltrials.gov. Unique identifier: NCT01013532.
Amniotic membrane transplantation for infectious keratitis: a systematic review and meta-analysis
Authors: Ting Darren Shu Jeng , Henein Christin , Said Dalia G. , Dua Harminder S. 
Published: June 2021

AbstractInfectious keratitis (IK) is the 5th leading cause of blindness globally. Broad-spectrum topical antimicrobial treatment is the current mainstay of treatment for IK, though adjuvant treatment or surgeries are often required in refractory cases of IK. This systematic review aimed to examine the effectiveness and safety of adjuvant amniotic membrane transplantation (AMT) for treating IK. Electronic databases, including MEDLINE, EMBASE and Cochrane Central, were searched for relevant articles. All clinical studies, including randomized controlled trials (RCTs), non-randomized controlled studies and case series (n > 5), were included. Primary outcome measure was time to complete corneal healing and secondary outcome measures included corrected-distance-visual-acuity (CDVA), uncorrected-distance-visual-acuity (UDVA), corneal vascularization and adverse events. A total of twenty-eight studies (including four RCTs) with 861 eyes were included. When compared to standard antimicrobial treatment alone, adjuvant AMT resulted in shorter mean time to complete corneal healing (− 4.08 days; 95% CI − 6.27 to − 1.88;p < 0.001) and better UDVA (− 0.26 logMAR; − 0.50 to − 0.02;p = 0.04) at 1 month follow-up in moderate-to-severe bacterial and fungal keratitis, with no significant difference in the risk of adverse events (risk ratio 0.80; 0.46–1.38;p = 0.42). One RCT demonstrated that adjuvant AMT resulted in better CDVA and less corneal vascularization at 6 months follow-up (bothp < 0.001). None of the RCTs examined the use of adjuvant AMT in herpetic or Acanthamoeba keratitis, though the benefit was supported by a number of case series. In conclusion, AMT serves as a useful adjuvant therapy in improving corneal healing and visual outcome in bacterial and fungal keratitis (low-quality evidence). Further adequately powered, high-quality RCTs are required to ascertain its therapeutic potential, particularly for herpetic and Acanthamoeba keratitis. Future standardization of the core outcome set in IK-related trials would be invaluable.
The short-term associations of chronic obstructive pulmonary disease hospitalizations with meteorological factors and air pollutants in Southwest China: a time-series study
Authors: Li Meng , Chen Shengqi , Zhao Hanqing , Tang Chengxiang , Lai Yunfeng , Ung Carolina Oi Lam , Su Jinya , Hu Hao 
Published: June 2021

AbstractChronic obstructive pulmonary disease (COPD) is the fourth major cause of mortality and morbidity worldwide and is projected to be the third by 2030. However, there is little evidence available on the associations of COPD hospitalizations with meteorological factors and air pollutants in developing countries/regions of Asia. In particular, no study has been done in western areas of China considering the nonlinear and lagged effects simultaneously. This study aims to evaluate the nonlinear and lagged associations of COPD hospitalizations with meteorological factors and air pollutants using time-series analysis. The modified associations by sex and age were also investigated. The distributed lag nonlinear model was used to establish the association of daily COPD hospitalizations of all 441 public hospitals in Chengdu, China from Jan/2015–Dec/2017 with the ambient meteorological factors and air pollutants. Model parameters were optimized based on quasi Akaike Information Criterion and model diagnostics was conducted by inspecting the deviance residuals. Subgroup analysis by sex and age was also performed. Temperature, relative humidity, wind and Carbon Monoxide (CO) have statistically significant and consistent associations with COPD hospitalizations. The cumulative relative risk (RR) was lowest at a temperature of 19℃ (relative humidity of 67%). Both extremely high and low temperature (and relative humidity) increase the cumulative RR. An increase of wind speed above 4 mph (an increase of CO above 1.44 mg/m3) significantly decreases (increases) the cumulative RR. Female populations were more sensitive to low temperature and high CO level; elderly (74+) populations are more sensitive to high relative humidity; younger populations (< = 74) are more susceptible to CO higher than 1.44 mg/m3. Therefore, people with COPD should avoid exposure to adverse environmental conditions of extreme temperatures and relative humidity, low wind speed and high CO level, especially for female and elderly patients who were more sensitive to extreme temperatures and relative humidity.
Plasma lipidomic analysis shows a disease progression signature in mdx mice
Authors: Tsonaka Roula , Seyer Alexandre , Aartsma-Rus Annemieke , Spitali Pietro 
Published: June 2021

AbstractDuchenne muscular dystrophy (DMD) is a rare genetic disorder affecting paediatric patients. The disease course is characterized by loss of muscle mass, which is rapidly substituted by fibrotic and adipose tissue. Clinical and preclinical models have clarified the processes leading to muscle damage and myofiber degeneration. Analysis of the fat component is however emerging as more evidence shows how muscle fat fraction is associated with patient performance and prognosis. In this article we aimed to study whether alterations exist in the composition of lipids in plasma samples obtained from mouse models. Analysis of plasma samples was performed in 4 mouse models of DMD and wild-type mice by LC–MS. Longitudinal samplings of individual mice covering an observational period of 7 months were obtained to cover the different phases of the disease. We report clear elevation of glycerolipids and glycerophospholipids families in dystrophic mice compared to healthy mice. Triacylglycerols were the strongest contributors to the signatures in mice. Annotation of individual lipids confirmed the elevation of lipids belonging to these families as strongest discriminants between healthy and dystrophic mice. A few sphingolipids (such as ganglioside GM2, sphingomyelin and ceramide), sterol lipids (such as cholesteryl oleate and cholesteryl arachidonate) and a fatty acyl (stearic acid) were also found to be affected in dystrophic mice. Analysis of serum and plasma samples show how several lipids are affected in dystrophic mice affected by muscular dystrophy. This study sets the basis to further investigations to understand how the lipid signature relates to the disease biology and muscle performance.
Accuracy Assessment of Two Electromagnetic Articulographs: Northern Digital Inc. WAVE and Northern Digital Inc. VOX
Authors: Rebernik Teja , Jacobi Jidde , Tiede Mark , Wieling Martijn 
Published: June 2021

Purpose
This study compares two electromagnetic articulographs manufactured by Northern Digital, Inc.: the NDI Wave System (from 2008) and the NDI Vox-EMA System (from 2020).

Method
Four experiments were completed: (a) comparison of statically positioned sensors, (b) tracking dynamic movements of sensors manipulated using a motor-driven LEGO apparatus, (c) tracking small and large movements of sensors mounted in a rigid bar manipulated by hand, and (d) tracking movements of sensors rotated on a circular disc. We assessed spatial variability for statically positioned sensors, variability in the transduced Euclidean distances between sensor pairs, and missing data rates. For sensors tracking circular movements, we compared the fit between fitted ideal circles and actual trajectories.

Results
The average sensor pair tracking error (i.e., the standard deviation of the Euclidean distances) was 1.37 mm for the WAVE and 0.12 mm for the VOX during automated trials at the fastest speed, and 0.35 mm for the WAVE and 0.14 mm for the VOX during the tracking of large manual movements. The average standard deviation of the fitted circle radii charted by manual circular disc movements was 0.72 mm for the WAVE sensors and 0.14 mm for the VOX sensors. There was no significant difference between the WAVE and the VOX in the number of missing frames.

Conclusions
In general, the VOX system significantly outperformed the WAVE on measures of both static precision and dynamic accuracy (automated and manual). For both systems, positional precision and spatial variability were influenced by the sensors' position relative to the field generator unit (worse when further away).

Supplemental Material

https://doi.org/10.23641/asha.14787846