bluuebunny/crossref_metadata_2025_split huggingface dataset:
Priority effects shape the structure of infant-typeBifidobacteriumcommunities on human milk oligosaccharides
Authors: Ojima Miriam N , Jiang Lin , Arzamasov Aleksandr A , Yoshida Keisuke , Odamaki Toshitaka , Xiao Jinzhong , Nakajima Aruto , Kitaoka Motomitsu , Hirose Junko , Urashima Tadasu , Katoh Toshihiko , Gotoh Aina , van Sinderen Douwe , Rodionov Dmitry A , Osterman Andrei L , Sakanaka Mikiyasu , Katayama Takane 
Published: June 2022

AbstractBifidobacteria are among the first colonizers of the infant gut, and human milk oligosaccharides (HMOs) in breastmilk are instrumental for the formation of a bifidobacteria-rich microbiota. However, little is known about the assembly of bifidobacterial communities. Here, by applying assembly theory to a community of four representative infant-gut associated Bifidobacterium species that employ varied strategies for HMO consumption, we show that arrival order and sugar consumption phenotypes significantly affected community formation. Bifidobacterium bifidum and Bifidobacterium longum subsp. infantis, two avid HMO consumers, dominate through inhibitory priority effects. On the other hand, Bifidobacterium breve, a species with limited HMO-utilization ability, can benefit from facilitative priority effects and dominates by utilizing fucose, an HMO degradant not utilized by the other bifidobacterial species. Analysis of publicly available breastfed infant faecal metagenome data showed that the observed trends for B. breve were consistent with our in vitro data, suggesting that priority effects may have contributed to its dominance. Our study highlights the importance and history dependency of initial community assembly and its implications for the maturation trajectory of the infant gut microbiota.
Gaps and opportunities in the treatment of relapsed-refractory multiple myeloma: Consensus recommendations of the NCI Multiple Myeloma Steering Committee
Authors: Kumar Shaji , Baizer Lawrence , Callander Natalie S. , Giralt Sergio A. , Hillengass Jens , Freidlin Boris , Hoering Antje , Richardson Paul G. , Schwartz Elena I. , Reiman Anthony , Lentzsch Suzanne , McCarthy Philip L. , Jagannath Sundar , Yee Andrew J. , Little Richard F. , Raje Noopur S. 
Published: June 2022

AbstractA wide variety of new therapeutic options for Multiple Myeloma (MM) have recently become available, extending progression-free and overall survival for patients in meaningful ways. However, these treatments are not curative, and patients eventually relapse, necessitating decisions on the appropriate choice of treatment(s) for the next phase of the disease. Additionally, an important subset of MM patients will prove to be refractory to the majority of the available treatments, requiring selection of effective therapies from the remaining options. Immunomodulatory agents (IMiDs), proteasome inhibitors, monoclonal antibodies, and alkylating agents are the major classes of MM therapies, with several options in each class. Patients who are refractory to one agent in a class may be responsive to a related compound or to a drug from a different class. However, rules for selection of alternative treatments in these situations are somewhat empirical and later phase clinical trials to inform those choices are ongoing. To address these issues the NCI Multiple Myeloma Steering Committee formed a relapsed/refractory working group to review optimal treatment choices, timing, and sequencing and provide recommendations. Additional issues considered include the role of salvage autologous stem cell transplantation, risk stratification, targeted approaches for genetic subsets of MM, appropriate clinical trial endpoints, and promising investigational agents. This report summarizes the deliberations of the working group and suggests potential avenues of research to improve the precision, timing, and durability of treatments for Myeloma.
A very-hot food and beverage thermal exposure index and esophageal cancer risk in Malawi and Tanzania: findings from the ESCCAPE case–control studies
Authors: Masukume Gwinyai , Mmbaga Blandina T. , Dzamalala Charles P. , Mlombe Yohannie B. , Finch Peter , Nyakunga-Maro Gissela , Mremi Alex , Middleton Daniel R. S. , Narh Clement T. , Chasimpha Steady J. D. , Abedi-Ardekani Behnoush , Menya Diana , Schüz Joachim , McCormack Valerie 
Published: June 2022

Abstract
Background
Consumption of very-hot beverages/food is a probable carcinogen. In East Africa, we investigated esophageal squamous cell carcinoma (ESCC) risk in relation to four thermal exposure metrics separately and in a combined score.

Methods
From the ESCCAPE case–control studies in Blantyre, Malawi (2017-20) and Kilimanjaro, Tanzania (2015-19), we used logistic regression models adjusted for country, age, sex, alcohol and tobacco, to estimate odds ratios (ORs) and 95% confidence intervals (CIs) for self-reported thermal exposures whilst consuming tea, coffee and/or porridge.

Results
The study included 849 cases and 906 controls. All metrics were positively associated with ESCC: temperature of drink/food (OR 1.92 (95% CI: 1.50, 2.46) for ‘very hot’ vs ‘hot’), waiting time before drinking/eating (1.76 (1.37, 2.26) for <2 vs 2–5 minutes), consumption speed (2.23 (1.78, 2.79) for ‘normal’ vs ‘slow’) and mouth burning (1.90 (1.19, 3.01) for ≥6 burns per month vs none). Amongst consumers, the composite score ranged from 1 to 12, and ESCC risk increased with higher scores, reaching an OR of 4.6 (2.1, 10.0) for scores of ≥9 vs 3.

Conclusions
Thermal exposure metrics were strongly associated with ESCC risk. Avoidance of very-hot food/beverage consumption may contribute to the prevention of ESCC in East Africa.
Two-band optical gain and ultrabright electroluminescence from colloidal quantum dots at 1000 A cm−2
Authors: Jung Heeyoung , Park Young-Shin , Ahn Namyoung , Lim Jaehoon , Fedin Igor , Livache Clément , Klimov Victor I. 
Published: June 2022

AbstractColloidal quantum dots (QDs) are attractive materials for the realization of solution-processable laser diodes. Primary challenges towards this objective are fast optical-gain relaxation due to nonradiative Auger recombination and poor stability of colloidal QD solids under high current densities required to obtain optical gain. Here we resolve these challenges and achieve broad-band optical gain spanning the band-edge (1S) and the higher-energy (1P) transitions. This demonstration is enabled by continuously graded QDs with strongly suppressed Auger recombination and a current-focusing device design, combined with short-pulse pumping. Using this approach, we achieve ultra-high current densities (~1000 A cm−2) and brightness (~10 million cd m−2), and demonstrate an unusual two-band electroluminescence regime for which the 1P band is more intense than the 1S feature. This implies the realization of extremely large QD occupancies of up to ~8 excitons per-dot, which corresponds to complete filling of the 1S and 1P electron shells.
Inactivation of the Hippo tumor suppressor pathway promotes melanoma
Authors: Vittoria Marc A. , Kingston Nathan , Kotynkova Kristyna , Xia Eric , Hong Rui , Huang Lee , McDonald Shayna , Tilston-Lunel Andrew , Darp Revati , Campbell Joshua D. , Lang Deborah , Xu Xiaowei , Ceol Craig J. , Varelas Xaralabos , Ganem Neil J. 
Published: June 2022

AbstractMelanoma is commonly driven by activating mutations in the MAP kinase BRAF; however, oncogenic BRAF alone is insufficient to promote melanomagenesis. Instead, its expression induces a transient proliferative burst that ultimately ceases with the development of benign nevi comprised of growth-arrested melanocytes. The tumor suppressive mechanisms that restrain nevus melanocyte proliferation remain poorly understood. Here we utilize cell and murine models to demonstrate that oncogenic BRAF leads to activation of the Hippo tumor suppressor pathway, both in melanocytes in vitro and nevus melanocytes in vivo. Mechanistically, we show that oncogenic BRAF promotes both ERK-dependent alterations in the actin cytoskeleton and whole-genome doubling events, which independently reduce RhoA activity to promote Hippo activation. We also demonstrate that functional impairment of the Hippo pathway enables oncogenic BRAF-expressing melanocytes to bypass nevus formation and rapidly form melanomas. Our data reveal that the Hippo pathway enforces the stable arrest of nevus melanocytes and represents a critical barrier to melanoma development.
Investigating water/oil interfaces with opto-thermophoresis
Authors: Kim Youngsun , Ding Hongru , Zheng Yuebing 
Published: June 2022

AbstractCharging of interfaces between water and hydrophobic media is a mysterious feature whose nature and origin have been under debate. Here, we investigate the fundamentals of the interfacial behaviors of water by employing opto-thermophoretic tweezers to study temperature-gradient-induced perturbation of dipole arrangement at water/oil interfaces. With surfactant-free perfluoropentane-in-water emulsions as a model interface, additional polar organic solvents are introduced to systematically modify the structural aspects of the interface. Through our experimental measurements on the thermophoretic behaviors of oil droplets under a light-generated temperature gradient, in combination with theoretical analysis, we propose that water molecules and mobile negative charges are present at the water/oil interfaces with specific dipole arrangement to hydrate oil droplets, and that this arrangement is highly susceptible to the thermal perturbation due to the mobility of the negative charges. These findings suggest a potential of opto-thermophoresis in probing aqueous interfaces and could enrich understanding of the interfacial behaviors of water.
Structure of the Dicer-2–R2D2 heterodimer bound to a small RNA duplex
Authors: Yamaguchi Sonomi , Naganuma Masahiro , Nishizawa Tomohiro , Kusakizako Tsukasa , Tomari Yukihide , Nishimasu Hiroshi , Nureki Osamu 
Published: June 2022

AbstractIn flies, Argonaute2 (Ago2) and small interfering RNA (siRNA) form an RNA-induced silencing complex to repress viral transcripts1. The RNase III enzyme Dicer-2 associates with its partner protein R2D2 and cleaves long double-stranded RNAs to produce 21-nucleotide siRNA duplexes, which are then loaded into Ago2 in a defined orientation2–5. Here we report cryo-electron microscopy structures of the Dicer-2–R2D2 and Dicer-2–R2D2–siRNA complexes. R2D2 interacts with the helicase domain and the central linker of Dicer-2 to inhibit the promiscuous processing of microRNA precursors by Dicer-2. Notably, our structure represents the strand-selection state in the siRNA-loading process, and reveals that R2D2 asymmetrically recognizes the end of the siRNA duplex with the higher base-pairing stability, and the other end is exposed to the solvent and is accessible by Ago2. Our findings explain how R2D2 senses the thermodynamic asymmetry of the siRNA and facilitates the siRNA loading into Ago2 in a defined orientation, thereby determining which strand of the siRNA duplex is used by Ago2 as the guide strand for target silencing.
Long-term observation of the egg and chick size in the nests of Larus ichthyaetus in Lake Chany, Russia
Authors: Yurlov Alexander K. , Yurlova Natalia I. , Garyushkina Maria Yu. , Selivanova Marina A. , Doi Hideyuki 
Published: June 2022

AbstractThis data set describes the long-term observation and morphological study of the eggs of the great black-headed gull Larus ichthyaetus in the gull nesting colonies on the islands of Lake Chany. Lake Chany is located in the Baraba forest-steppe of the West Siberian Plain, Russia, between the Ob and Irtish rivers. Lake Chany is protected by the Ramsar Convention on the Wetlands of International Importance, indicating that the lake is an important site for migratory birds, including L. ichthyaetus. This dataset contains the size and fate of all eggs, as well as the size of hatched chicks in 1164 observed L. ichthyaetus nests from 1993 to 2003.
Confined acoustic line modes within a glide-symmetric waveguide
Authors: Moore Daniel B. , Ward Gareth P. , Smith John D. , Hibbins Alastair P. , Sambles J. Roy , Starkey Timothy A. 
Published: June 2022

AbstractConfined coupled acoustic line-modes supported by two parallel lines of periodic holes on opposite surfaces of a glide-symmetric waveguide have a hybrid character combining symmetric and anti-symmetric properties. These hybrid coupled acoustic line-modes have a near constant group velocity over a broad frequency range as no band gap is formed at the first Brillouin zone boundary. We show that the hybrid character of these confined modes is tuneable as a function of the spacing between the two surfaces. Further we explore how the band-gap reappears as the glide symmetry is broken.
Spatial patterns and climate drivers of malaria in three border areas of Brazil, Venezuela and Guyana, 2016–2018
Authors: Wangdi Kinley , Wetzler Erica , Cox Horace , Marchesini Paola , Villegas Leopoldo , Canavati Sara 
Published: June 2022

AbstractIn 2020, 77% of malaria cases in the Americas were concentrated in Venezuela, Brazil, and Colombia. These countries are characterized by a heterogeneous malaria landscape and malaria hotspots. Furthermore, the political unrest in Venezuela has led to significant cross-border population movement. Hence, the aim of this study was to describe spatial patterns and identify significant climatic drivers of malaria transmission along the Venezuela-Brazil-Guyana border, focusing on Bolivar state, Venezuela and Roraima state, Brazil. Malaria case data, stratified by species from 2016 to 2018, were obtained from the Brazilian Malaria Epidemiology Surveillance Information System, the Guyana Vector Borne Diseases Program, the Venezuelan Ministry of Health, and civil society organizations. Spatial autocorrelation in malaria incidence was explored using Getis-Ord (Gi*) statistics. A Poisson regression model was developed with a conditional autoregressive prior structure and posterior parameters were estimated using the Bayesian Markov chain Monte Carlo simulation with Gibbs sampling. There were 685,498 malaria cases during the study period.Plasmodium vivaxwas the predominant species (71.7%, 490,861). Malaria hotspots were located in eight municipalities along the Venezuela and Guyana international borders with Brazil.Plasmodium falciparumincreased by 2.6% (95% credible interval [CrI] 2.1%, 2.8%) for one meter increase in altitude, decreased by 1.6% (95% CrI 1.5%, 2.3%) and 0.9% (95% CrI 0.7%, 2.4%) per 1 cm increase in 6-month lagged precipitation and each 1 °C increase of minimum temperature without lag. Each 1 °C increase of 1-month lagged maximum temperature increasedP. falciparumby 0.6% (95% CrI 0.4%, 1.9%).P. vivaxcases increased by 1.5% (95% CrI 1.3%, 1.6%) for one meter increase in altitude and decreased by 1.1% (95% CrI 1.0%, 1.2%) and 7.3% (95% CrI 6.7%, 9.7%) for each 1 cm increase of precipitation lagged at 6-months and 1 °C increase in minimum temperature lagged at 6-months. Each 1°C increase of two-month lagged maximum temperature increasedP. vivaxby 1.5% (95% CrI 0.6%, 7.1%). There was no significant residual spatial clustering after accounting for climatic covariates. Malaria hotspots were located along the Venezuela and Guyana international border with Roraima state, Brazil. In addition to population movement, climatic variables were important drivers of malaria transmission in these areas.
Quantitative systems pharmacology modeling sheds light into the dose response relationship of a trispecific T cell engager in multiple myeloma
Authors: Abrams R. E. , Pierre K. , El-Murr N. , Seung E. , Wu L. , Luna E. , Mehta R. , Li J. , Larabi K. , Ahmed M. , Pelekanou V. , Yang Z.-Y. , van de Velde H. , Stamatelos S. K. 
Published: June 2022

AbstractIn relapsed and refractory multiple myeloma (RRMM), there are few treatment options once patients progress from the established standard of care. Several bispecific T-cell engagers (TCE) are in clinical development for multiple myeloma (MM), designed to promote T-cell activation and tumor killing by binding a T-cell receptor and a myeloma target. In this study we employ both computational and experimental tools to investigate how a novel trispecific TCE improves activation, proliferation, and cytolytic activity of T-cells against MM cells. In addition to binding CD3 on T-cells and CD38 on tumor cells, the trispecific binds CD28, which serves as both co-stimulation for T-cell activation and an additional tumor target. We have established a robust rule-based quantitative systems pharmacology (QSP) model trained against T-cell activation, cytotoxicity, and cytokine data, and used it to gain insight into the complex dose response of this drug. We predict that CD3-CD28-CD38 killing capacity increases rapidly in low dose levels, and with higher doses, killing plateaus rather than following the bell-shaped curve typical of bispecific TCEs. We further predict that dose–response curves are driven by the ability of tumor cells to form synapses with activated T-cells. When competition between cells limits tumor engagement with active T-cells, response to therapy may be diminished. We finally suggest a metric related to drug efficacy in our analysis—“effective” receptor occupancy, or the proportion of receptors engaged in synapses. Overall, this study predicts that the CD28 arm on the trispecific antibody improves efficacy, and identifies metrics to inform potency of novel TCEs.
Foot contact forces can be used to personalize a wearable robot during human walking
Authors: Jacobson Michael , Kantharaju Prakyath , Jeong Hyeongkeun , Ryu Jae-Kwan , Park Jung-Jae , Chung Hyun-Joon , Kim Myunghee 
Published: June 2022

AbstractIndividuals with below-knee amputation (BKA) experience increased physical effort when walking, and the use of a robotic ankle-foot prosthesis (AFP) can reduce such effort. The walking effort could be further reduced if the robot is personalized to the wearer using human-in-the-loop (HIL) optimization of wearable robot parameters. The conventional physiological measurement, however, requires a long estimation time, hampering real-time optimization due to the limited experimental time budget. This study hypothesized that a function of foot contact force, the symmetric foot force-time integral (FFTI), could be used as a cost function for HIL optimization to rapidly estimate the physical effort of walking. We found that the new cost function presents a reasonable correlation with measured metabolic cost. When we employed the new cost function in HIL ankle-foot prosthesis stiffness parameter optimization, 8 individuals with simulated amputation reduced their metabolic cost of walking, greater than 15% (p < 0.02), compared to the weight-based and control-off conditions. The symmetry cost using the FFTI percentage was lower for the optimal condition, compared to all other conditions (p < 0.05). This study suggests that foot force-time integral symmetry using foot pressure sensors can be used as a cost function when optimizing a wearable robot parameter.
Poroelastic properties of rocks with a comparison of theoretical estimates and typical experimental results
Authors: Selvadurai A. P. S. , Suvorov A. P. 
Published: June 2022

AbstractThe paper develops theoretical estimates for the parameters that describe the classical theory of poroelasticity for a fluid-saturated porous medium, with a porous elastic skeleton that can exhibit imperfect grain contacts. The results for the poroelastic properties predicted from the modelling are compared with experimental results available in the literature.
Photosystem stoichiometry adjustment is a photoreceptor-mediated process in Arabidopsis
Authors: Ibrahim Iskander M. , McKenzie Steven D. , Chung Jae , Aryal Uma K. , Leon-Salas Walter D. , Puthiyaveetil Sujith 
Published: June 2022

AbstractPlant growth under spectrally-enriched low light conditions leads to adjustment in the relative abundance of the two photosystems in an acclimatory response known as photosystem stoichiometry adjustment. Adjustment of photosystem stoichiometry improves the quantum efficiency of photosynthesis but how this process perceives light quality changes and how photosystem amount is regulated remain largely unknown. By using a label-free quantitative mass spectrometry approach in Arabidopsis here we show that photosystem stoichiometry adjustment is primarily driven by the regulation of photosystem I content and that this forms the major thylakoid proteomic response under light quality. Using light and redox signaling mutants, we further show that the light quality-responsive accumulation of photosystem I gene transcripts and proteins requires phytochrome B photoreceptor but not plastoquinone redox signaling as previously suggested. In far-red light, the increased acceptor side limitation might deplete active photosystem I pool, further contributing to the adjustment of photosystem stoichiometry.
Multiparameter laser performance characterization of liquid crystals for polarization control devices in the nanosecond regime
Authors: Marshall Kenneth L. , Kafka Kyle R. P. , Urban Nathaniel D. , Wallace Jason U. , Demos Stavros G. 
Published: June 2022

AbstractInteractions of liquid crystals (LC’s) with polarized light have been studied widely and have spawned numerous device applications, including the fabrication of optical elements for high-power and large-aperture laser systems. Currently, little is known about both the effect of incident polarization state on laser-induced–damage threshold (LIDT) and laser-induced functional threshold (LIFT) behavior at sub-LIDT fluences under multipulse irradiation conditions. This work reports on the first study of the nanosecond-pulsed LIDT’s dependence on incident polarization for several optical devices employing oriented nematic and chiral-nematic LC’s oriented by surface alignment layers. Accelerated lifetime testing was also performed to characterize the ability of these devices to maintain their functional performance under multipulse irradiation as a function of the laser fluence at both 1053 nm and 351 nm. Results show that the LIDT varies as a function of input polarization by 30–80% within the same device, while the multipulse LIFT (which can differ from the nominal LIDT) depends on irradiation conditions such as laser fluence and wavelength.
HEAT SHOCK TRANSCRIPTION FACTOR B2b acts as a transcriptional repressor of VIN3, a gene induced by long-term cold for flowering
Authors: Jeong Goowon , Jeon Myeongjune , Shin Jinwoo , Lee Ilha 
Published: June 2022

AbstractVernalization, an acceleration of flowering after long-term winter cold, is an intensively studied flowering mechanism in winter annual plants. In Arabidopsis, Polycomb Repressive Complex 2 (PRC2)-mediated suppression of the strong floral repressor, FLOWERING LOCUS C (FLC), is critical for vernalization and a PHD finger domain protein, VERNALIZATION INSENSITIVE 3 (VIN3), recruits PRC2 on FLC chromatin. The level of VIN3 was found to gradually increase in proportion to the length of cold period during vernalization. However, how plants finely regulate VIN3 expression according to the cold environment has not been completely elucidated. As a result, we performed EMS mutagenesis using a transgenic line with a minimal promoter of VIN3 fused to the GUS reporter gene, and isolated a mutant, hyperactivation of VIN3 1 (hov1), which showed increased GUS signal and endogenous VIN3 transcript levels. Using positional cloning combined with whole-genome resequencing, we found that hov1 carries a nonsense mutation, leading to a premature stop codon on the HEAT SHOCK TRANSCRIPTION FACTOR B2b (HsfB2b), which encodes a repressive heat shock transcription factor. HsfB2b directly binds to the VIN3 promoter, and HsfB2b overexpression leads to reduced acceleration of flowering after vernalization. Collectively, our findings reveal a novel fine-tuning mechanism to regulate VIN3 for proper vernalization response.