bluuebunny/crossref_metadata_2025_split huggingface dataset:
DAXX-ATRX regulation of p53 chromatin binding and DNA damage response
Authors: Gulve Nitish , Su Chenhe , Deng Zhong , Soldan Samantha S. , Vladimirova Olga , Wickramasinghe Jayamanna , Zheng Hongwu , Kossenkov Andrew V. , Lieberman Paul. M. 
Published: August 2022

AbstractDAXX and ATRX are tumor suppressor proteins that form a histone H3.3 chaperone complex and are frequently mutated in cancers with the alternative lengthening of telomeres (ALT). Here, we show that DAXX and ATRX knock-out (KO) U87-T cells that have acquired ALT-like features have defects in p53 chromatin binding and DNA damage response. RNA-seq analysis revealed that p53 pathway is among the most perturbed. ChIP-seq and ATAC-seq revealed a genome-wide reduction in p53 DNA-binding and corresponding loss of chromatin accessibility at many p53 response elements across the genome. Both DAXX and ATRX null cells showed a depletion of histone H3.3 and accumulation of γH2AX at many p53 sites, including subtelomeres. These findings indicate that loss of DAXX or ATRX can compromise p53 chromatin binding and p53 DNA damage response in ALT-like cells, providing a link between histone composition, chromatin accessibility and tumor suppressor function of p53.
Touchless interactive teaching of soft robots through flexible bimodal sensory interfaces
Authors: Liu Wenbo , Duo Youning , Liu Jiaqi , Yuan Feiyang , Li Lei , Li Luchen , Wang Gang , Chen Bohan , Wang Siqi , Yang Hui , Liu Yuchen , Mo Yanru , Wang Yun , Fang Bin , Sun Fuchun , Ding Xilun , Zhang Chi , Wen Li 
Published: August 2022

AbstractIn this paper, we propose a multimodal flexible sensory interface for interactively teaching soft robots to perform skilled locomotion using bare human hands. First, we develop a flexible bimodal smart skin (FBSS) based on triboelectric nanogenerator and liquid metal sensing that can perform simultaneous tactile and touchless sensing and distinguish these two modes in real time. With the FBSS, soft robots can react on their own to tactile and touchless stimuli. We then propose a distance control method that enabled humans to teach soft robots movements via bare hand-eye coordination. The results showed that participants can effectively teach a self-reacting soft continuum manipulator complex motions in three-dimensional space through a “shifting sensors and teaching” method within just a few minutes. The soft manipulator can repeat the human-taught motions and replay them at different speeds. Finally, we demonstrate that humans can easily teach the soft manipulator to complete specific tasks such as completing a pen-and-paper maze, taking a throat swab, and crossing a barrier to grasp an object. We envision that this user-friendly, non-programmable teaching method based on flexible multimodal sensory interfaces could broadly expand the domains in which humans interact with and utilize soft robots.
Directed evolution of phosphite dehydrogenase to cycle noncanonical redox cofactors via universal growth selection platform
Authors: Zhang Linyue , King Edward , Black William B. , Heckmann Christian M. , Wolder Allison , Cui Youtian , Nicklen Francis , Siegel Justin B. , Luo Ray , Paul Caroline E. , Li Han 
Published: August 2022

AbstractNoncanonical redox cofactors are attractive low-cost alternatives to nicotinamide adenine dinucleotide (phosphate) (NAD(P)+) in biotransformation. However, engineering enzymes to utilize them is challenging. Here, we present a high-throughput directed evolution platform which couples cell growth to the in vivo cycling of a noncanonical cofactor, nicotinamide mononucleotide (NMN+). We achieve this by engineering the life-essential glutathione reductase in Escherichia coli to exclusively rely on the reduced NMN+ (NMNH). Using this system, we develop a phosphite dehydrogenase (PTDH) to cycle NMN+ with ~147-fold improved catalytic efficiency, which translates to an industrially viable total turnover number of ~45,000 in cell-free biotransformation without requiring high cofactor concentrations. Moreover, the PTDH variants also exhibit improved activity with another structurally deviant noncanonical cofactor, 1-benzylnicotinamide (BNA+), showcasing their broad applications. Structural modeling prediction reveals a general design principle where the mutations and the smaller, noncanonical cofactors together mimic the steric interactions of the larger, natural cofactors NAD(P)+.
Inequality can double the energy required to secure universal decent living
Authors: Millward-Hopkins Joel 
Published: August 2022

AbstractEcological breakdown and economic inequality are among the largest contemporary global challenges, and the issues are thoroughly entangled – as they have been throughout the history of civilisations. Yet, the global economy continues toward ecological crises, and inequalities remain far higher than citizens believe to be fair. Here, we explore the role of inequality, alongside traditional drivers of ecological impacts, in determining global energy requirements for providing universal decent living. We consider scenarios from fair inequality – where inequalities mirror public ideals – through a fairly unequal world, to one with a super-rich global elite. The energy-costs of inequality appear far more significant than population: even fair levels increase the energy required to provide universal decent living by 40%, and a super-rich global 1% could consume as much energy as would providing decent living to 1.7 billion. We finish by arguing that total population remains important nonetheless, but for reasons beyond ecological impacts.
Perforin-2 clockwise hand-over-hand pre-pore to pore transition mechanism
Authors: Jiao Fang , Dehez François , Ni Tao , Yu Xiulian , Dittman Jeremy S. , Gilbert Robert , Chipot Christophe , Scheuring Simon 
Published: August 2022

AbstractPerforin-2 (PFN2, MPEG1) is a pore-forming protein that acts as a first line of defense in the mammalian immune system, rapidly killing engulfed microbes within the phagolysosome in macrophages. PFN2 self-assembles into hexadecameric pre-pore rings that transition upon acidification into pores damaging target cell membranes. Here, using high-speed atomic force microscopy (HS-AFM) imaging and line-scanning and molecular dynamics simulation, we elucidate PFN2 pre-pore to pore transition pathways and dynamics. Upon acidification, the pre-pore rings (pre-pore-I) display frequent, 1.8 s−1, ring-opening dynamics that eventually, 0.2 s−1, initiate transition into an intermediate, short-lived, ~75 ms, pre-pore-II state, inducing a clockwise pre-pore-I to pre-pore-II propagation. Concomitantly, the first pre-pore-II subunit, undergoes a major conformational change to the pore state that propagates also clockwise at a rate ~15 s−1. Thus, the pre-pore to pore transition is a clockwise hand-over-hand mechanism that is accomplished within ~1.3 s. Our findings suggest a clockwise mechanism of membrane insertion that with variations may be general for the MACPF/CDC superfamily.
Liquid-infused microstructured bioadhesives halt non-compressible hemorrhage
Authors: Bao Guangyu , Gao Qiman , Cau Massimo , Ali-Mohamad Nabil , Strong Mitchell , Jiang Shuaibing , Yang Zhen , Valiei Amin , Ma Zhenwei , Amabili Marco , Gao Zu-Hua , Mongeau Luc , Kastrup Christian , Li Jianyu 
Published: August 2022

AbstractNon-compressible hemorrhage is an unmet clinical challenge that accounts for high mortality in trauma. Rapid pressurized blood flows under hemorrhage impair the function and integrity of hemostatic agents and the adhesion of bioadhesive sealants. Here, we report the design and performance of bioinspired microstructured bioadhesives, formed with a macroporous tough xerogel infused with functional liquids. The xerogel can rapidly absorb interfacial fluids such as whole blood and promote blood clotting, while the infused liquids facilitate interfacial bonding, sealing, and antibacterial function. Their synergy enables the bioadhesives to form tough adhesion on ex vivo human and porcine tissues and diverse engineered surfaces without the need for compression, as well as on-demand instant removal and storage stability. We demonstrate a significantly improved hemostatic efficacy and biocompatibility in rats and pigs compared to non-structured counterparts and commercial products. This work opens new avenues for the development of bioadhesives and hemostatic sealants.
Whole-exome analysis of 177 pediatric patients with undiagnosed diseases
Authors: Narita Kotaro , Muramatsu Hideki , Narumi Satoshi , Nakamura Yuji , Okuno Yusuke , Suzuki Kyogo , Hamada Motoharu , Yamaguchi Naoya , Suzuki Atsushi , Nishio Yosuke , Shiraki Anna , Yamamori Ayako , Tsumura Yusuke , Sawamura Fumi , Kawaguchi Masahiro , Wakamatsu Manabu , Kataoka Shinsuke , Kato Kohji , Asada Hideyuki , Kubota Tetsuo , Muramatsu Yukako , Kidokoro Hiroyuki , Natsume Jun , Mizuno Seiji , Nakata Tomohiko , Inagaki Hidehito , Ishihara Naoko , Yonekawa Takahiro , Okumura Akihisa , Ogi Tomoo , Kojima Seiji , Kaname Tadashi , Hasegawa Tomonobu , Saitoh Shinji , Takahashi Yoshiyuki 
Published: August 2022

AbstractRecently, whole-exome sequencing (WES) has been used for genetic diagnoses of patients who remain otherwise undiagnosed. WES was performed in 177 Japanese patients with undiagnosed conditions who were referred to the Tokai regional branch of the Initiative on Rare and Undiagnosed Diseases (IRUD) (TOKAI-IRUD). This study included only patients who had not previously received genome-wide testing. Review meetings with specialists in various medical fields were held to evaluate the genetic diagnosis in each case, which was based on the guidelines of the American College of Medical Genetics and Genomics. WES identified diagnostic single-nucleotide variants in 66 patients and copy number variants (CNVs) in 11 patients. Additionally, a patient was diagnosed with Angelman syndrome with a complex clinical phenotype upon detection of a paternally derived uniparental disomy (UPD) [upd(15)pat] wherein the patient carried a homozygous DUOX2 p.E520D variant in the UPD region. Functional analysis confirmed that this DUOX2 variant was a loss-of-function missense substitution and the primary cause of congenital hypothyroidism. A significantly higher proportion of genetic diagnoses was achieved compared to previous reports (44%, 78/177 vs. 24–35%, respectively), probably due to detailed discussions and the higher rate of CNV detection.
Contactless doping characterization of $${\mathrm{Ga}_{2}\mathrm{O}_{3}}$$ using acceptor Cd probes
Authors: Barbosa Marcelo B. , Correia João Guilherme , Lorenz Katharina , Lopes Armandina M. L. , Oliveira Gonçalo N. P. , Fenta Abel S. , Schell Juliana , Teixeira Ricardo , Nogales Emilio , Méndez Bianchi , Stroppa Alessandro , Araújo João Pedro 
Published: August 2022

AbstractFinding suitable p-type dopants, as well as reliable doping and characterization methods for the emerging wide bandgap semiconductor $$\beta$$
β
-$${\mathrm{Ga}_{2}\mathrm{O}_{3}}$$

Ga
2

O
3

could strongly influence and contribute to the development of the next generation of power electronics. In this work, we combine easily accessible ion implantation, diffusion and nuclear transmutation methods to properly incorporate the Cd dopant into the $$\beta$$
β
-$${\mathrm{Ga}_{2}\mathrm{O}_{3}}$$

Ga
2

O
3

lattice, being subsequently characterized at the atomic scale with the Perturbed Angular Correlation (PAC) technique and Density Functional Theory (DFT) simulations. The acceptor character of Cd in $$\beta$$
β
-$${\mathrm{Ga}_{2}\mathrm{O}_{3}}$$

Ga
2

O
3

is demonstrated, with Cd sitting in the octahedral Ga site having a negative charge state, showing no evidence of polaron deformations nor extra point defects nearby. The possibility to determine the charge state of Cd will allow assessing the doping type, in particular proving p-type character, without the need for ohmic contacts. Furthermore, a possible approach for contactless charge mobility studies is demonstrated, revealing thermally activated free electrons for temperatures above $$\sim$$
∼
648 K with an activation energy of 0.54(1) and local electron transport dominated by a tunneling process between defect levels and the Cd probes at lower temperatures.
Feasibility of low-cost particle sensor types in long-term indoor air pollution health studies after repeated calibration, 2019–2021
Authors: Anastasiou Elle , Vilcassim M. J. Ruzmyn , Adragna John , Gill Emily , Tovar Albert , Thorpe Lorna E. , Gordon Terry 
Published: August 2022

AbstractPrevious studies have explored using calibrated low-cost particulate matter (PM) sensors, but important research gaps remain regarding long-term performance and reliability. Evaluate longitudinal performance of low-cost particle sensors by measuring sensor performance changes over 2 years of use. 51 low-cost particle sensors (Airbeam 1 N = 29; Airbeam 2 N = 22) were calibrated four times over a 2-year timeframe between 2019 and 2021. Cigarette smoke-specific calibration curves for Airbeam 1 and 2 PM sensors were created by directly comparing simultaneous 1-min readings of a Thermo Scientific Personal DataRAM PDR-1500 unit with a 2.5 µm inlet. Inter-sensor variability in calibration coefficient was high, particularly in Airbeam 1 sensors at study initiation. Calibration coefficients for both sensor types trended downwards over time to < 1 at final calibration timepoint [Airbeam 1 Mean (SD) = 0.87 (0.20); Airbeam 2 Mean (SD) = 0.96 (0.27)]. We lost more Airbeam 1 sensors (N = 27 out of 56, failure rate 48.2%) than Airbeam 2 (N = 2 out of 24, failure rate 8.3%) due to electronics, battery, or data output issues. Evidence suggests degradation over time might depend more on particle sensor type, rather than individual usage. Repeated calibrations of low-cost particle sensors may increase confidence in reported PM levels in longitudinal indoor air pollution studies.
Phenome of coeliac disease vs. inflammatory bowel disease
Authors: Kleinjans Moritz , Schneider Carolin V. , Bruns Tony , Strnad Pavel 
Published: August 2022

AbstractCoeliac disease (CeD) is characterized by gliadin-induced intestinal inflammation appearing in genetically susceptible individuals, such as HLA-DQ2.5 carriers. CeD, as well as other chronic intestinal disorders, such as Crohn's disease (CD) and ulcerative colitis, has been associated with increased morbidity and mortality, but the causes are unknown. We systematically analysed CeD-associated diagnoses and compared them to conditions enriched in subjects with CD/UC as well as in HLA-DQ2.5 carriers without CeD. We compared the overall and cause-specific mortality and morbidity of 3,001 patients with CeD, 2,020 with CD, 4,399 with UC and 492,200 controls in the community-based UK Biobank. Disease-specific phenotypes were assessed with the multivariable Phenome Wide Association Study (PheWAS) method. Associations were adjusted for age, sex and body mass index. All disease groups displayed higher overall mortality than controls (CD: aHR = 1.91[1.70–2.17]; UC: aHR = 1.32 [1.20–1.46]; CeD: aHR = 1.38 [1.22–1.55]). Cardiovascular and cancer-related deaths were responsible for the majority of fatalities. PheWAS analysis revealed 166 Phecodes overrepresented in all three disorders, whereas only ~ 20% of enriched Phecodes were disease specific. Seven of the 58 identified CeD-specific Phecodes were enriched in individuals homozygous for HLA-DQ2.5 without diagnosed CeD. Four out of these seven Phecodes and eight out of 19 HLA-DQ2.5 specific Phecodes were more common in homozygous HLA-DQ2.5 subjects with vs. without CeD, highlighting the interplay between genetics and diagnosis-related factors. Our study illustrates that the morbidity and mortality in CeD share similarities with CD/UC, while the CeD-restricted conditions might be driven by both inherited and acquired factors.
Quality and timeliness of emergency obstetric care and its association with maternal outcome in Keren Hospital, Eritrea
Authors: Zewde Henos Kiflom 
Published: August 2022

AbstractDespite the critical role quality comprehensive emergency obstetric care (CEmOC) plays in ensuring safe motherhood, only a few studies have attempted to measure the impact of substandard and delayed care on maternal outcome thus far. This study evaluates the association between various process and timeliness indicators of CEmOC and adverse maternal outcome in Keren Hospital. This study compared women with potentially life-threatening condition (PLTC) and women with severe maternal outcome (SMO) with respect to various process and timeliness indicators. Logistic regression analysis was employed to assess the association of timeliness and process indicators with SMO using SPSS version-22 computer software. In this study, we included 491 cases of PLTC and 210 cases of SMO (171 maternal near misses and 39 maternal deaths). The following process indicators showed significant association with SMO: failure to give uterotonics for the treatment of postpartum hemorrhage, failure to administer prophylactic antibiotics, and delayed laporatomy for uterine rupture. Moreover, delays in referral, triaging, seeing an obstetrician, and receiving definitive treatement were strongly associated with SMO. The following causes of delay were also found to be independently associated with SMO: erroneous diagnosis, inappropriate management, multiple referrals between health facilities, unavailability of a senior obstetrician, and poor communication during referral. Among the miscellaneous factors, nighttime admission and referral during the rainy season showed significant association with SMO. Findings of this study indicate that huge gap exists in providing quality and timely care in Keren Hospital. In general, most incidents of substandard and delayed care were due to poor referral system, insufficiency of medical staff, inadequacy of drugs and equipment, and unavailability of standard management protocol. Improving the referral system, upgrading the technical skills of health professionals, making sure life-saving drugs and equipment are available all the time, and posting standard treatment and management protocols in the maternity and emergency rooms will play a vital role in reducing the occurrence of SMO in Keren Hospital.
Relationship between serum 25 hydroxyvitamin D (25(OH)D) levels and mental health in shift female nurses
Authors: Tang Hsin-Ya , Ko Wang-Sheng , Yan Yuan-Horng , Yu Su-Chen , Chiou Ya-ling 
Published: August 2022

AbstractThe nurses work long hours and in various shifts, and often accompanied by depression, fatigue, and sleep disorders. Many studies have found that 25 hydroxyvitamin D (25(OH)D) is related to mental health. We aimed to investigate the relationship between depression, sleep problems, fatigue, and serum 25(OH)D levels in shift nurses. We recruited 34 day-shift, 30 evening-shift and 31 night-shift nurses. The Beck Depression Inventory II (BDI-II), Numerical Rating Scale and General Sleep Disturbance Scale to evaluate the levels of depression, sleep problems, fatigue. Blood samples (20 ml) were collected under a fasting state to determine basic biochemistry and inflammatory parameters. In central of Taiwan, approximately 96.1% of shift nurses had deficient (< 20 ng/ml) (45 females and 1 male) and inadequate (20–29 ng/ml) (39 females and 2 male) 25(OH)D levels. Approximately 84.2% of shift nurses experienced fatigue. In sleep disturbance, night-shift nurses experienced significantly more severe sleep disturbance than day-shift and evening-shift nurses. However, no significant correlation was observed between 25(OH)D levels and mental health when the 25(OH)D level was categorized. 25(OH)D deficiency, sleep disturbance, depression, and fatigue were common in shift female nurses, but it was not possible to demonstrate the impact of 25(OH)D deficiency on the mental health of shift nurses in Taiwan.
Experimental characterization of $${\text {H}}_2$$/water multiphase flow in heterogeneous sandstone rock at the core scale relevant for underground hydrogen storage (UHS)
Authors: Boon Maartje , Hajibeygi Hadi 
Published: August 2022

AbstractGeological porous reservoirs provide the volume capacity needed for large scale underground hydrogen storage (UHS). To effectively exploit these reservoirs for UHS, it is crucial to characterize the hydrogen transport properties inside porous rocks. In this work, for the first time in the community, we have performed $${\text {H}}_2$$

H
2

/water multiphase flow experiments at core scale under medical X-ray CT scanner. This has allowed us to directly image the complex transport properties of $${\text {H}}_2$$

H
2

when it is injected or retracted from the porous rock. The important effective functions of capillary pressure and relative permeability are also measured, for both drainage and imbibition. The capillary pressure measurements are combined with MICP data to derive a receding contact angle for the $${\text {H}}_2$$

H
2

/water/sandstone rock system. The rock core sample is a heterogeneous Berea sandstone (17 cm long and 3.8 cm diameter). Our investigation reveals the interplay between gravitational, capillary, and viscous forces. More specifically, it illustrates complex displacement patterns in the rock, including gravity segregation, enhancement of spreading of $${\text {H}}_2$$

H
2

due to capillary barriers, and the formation of fingers/channel during imbibition which lead to significant trapping of hydrogen. These findings shed new light on our fundamental understanding of the transport characteristics of $${\text {H}}_2$$

H
2

/water relevant for UHS.
Distance-based paper device using combined SYBR safe and gold nanoparticle probe LAMP assay to detect Leishmania among patients with HIV
Authors: Ruang-areerate Toon , Saengsawang Natkrittaya , Ruang-areerate Panthita , Ratnarathorn Nalin , Thita Thanyapit , Leelayoova Saovanee , Siripattanapipong Suradej , Choowongkomon Kiattawee , Dungchai Wijitar 
Published: August 2022

AbstractAsymptomatic visceral leishmaniasis cases increase continuously, particularly among patients with HIV who are at risk to develop further symptoms of leishmaniasis. A simple, sensitive and reliable diagnosis is crucially needed due to risk populations mostly residing in rural communities with limited resources of laboratory equipment. In this study, a highly sensitive and selective determination of Leishmania among asymptomatic patients with Leishmania/HIV co-infection was achieved to simultaneously interpret and semi-quantify using colorimetric precipitates (gold-nanoparticle probe; AuNP-probe) and fluorescence (SYBR safe dye and distance-based paper device; dPAD) in one-step loop-mediated isothermal amplification (LAMP) assay. The sensitivities and specificities of 3 detection methods were equivalent and had reliable performances achieving as high as 95.5%. Detection limits were 102 parasites/mL (0.0147 ng/µL) which were 10 times more sensitive than other related studies. To empower leishmaniasis surveillance as well as prevention and control, this dPAD combined with SYBR safe and gold nanoparticle probe LAMP assay is reliably fast, simple, inexpensive and practical for field diagnostics to point-of-care settings in resource-limited areas which can be set up in all levels of healthcare facilities, especially in low to middle income countries.