bluuebunny/crossref_metadata_2025_split huggingface dataset:
Sub-optical-cycle light-matter energy transfer in molecular vibrational spectroscopy
Authors: Peschel Martin T. , Högner Maximilian , Buberl Theresa , Keefer Daniel , de Vivie-Riedle Regina , Pupeza Ioachim 
Published: October 2022

AbstractThe evolution of ultrafast-laser technology has steadily advanced the level of detail in studies of light-matter interactions. Here, we employ electric-field-resolved spectroscopy and quantum-chemical modelling to precisely measure and describe the complete coherent energy transfer between octave-spanning mid-infrared waveforms and vibrating molecules in aqueous solution. The sub-optical-cycle temporal resolution of our technique reveals alternating absorption and (stimulated) emission on a few-femtosecond time scale. This behaviour can only be captured when effects beyond the rotating wave approximation are considered. At a femtosecond-to-picosecond timescale, optical-phase-dependent coherent transients and the dephasing of the vibrations of resonantly excited methylsulfonylmethane (DMSO2) are observed. Ab initio modelling using density functional theory traces these dynamics back to molecular-scale sample properties, in particular vibrational frequencies and transition dipoles, as well as their fluctuation due to the motion of DMSO2 through varying solvent environments. Future extension of our study to nonlinear interrogation of higher-order susceptibilities is fathomable with state-of-the-art lasers.
Using domain knowledge for robust and generalizable deep learning-based CT-free PET attenuation and scatter correction
Authors: Guo Rui , Xue Song , Hu Jiaxi , Sari Hasan , Mingels Clemens , Zeimpekis Konstantinos , Prenosil George , Wang Yue , Zhang Yu , Viscione Marco , Sznitman Raphael , Rominger Axel , Li Biao , Shi Kuangyu 
Published: October 2022

AbstractDespite the potential of deep learning (DL)-based methods in substituting CT-based PET attenuation and scatter correction for CT-free PET imaging, a critical bottleneck is their limited capability in handling large heterogeneity of tracers and scanners of PET imaging. This study employs a simple way to integrate domain knowledge in DL for CT-free PET imaging. In contrast to conventional direct DL methods, we simplify the complex problem by a domain decomposition so that the learning of anatomy-dependent attenuation correction can be achieved robustly in a low-frequency domain while the original anatomy-independent high-frequency texture can be preserved during the processing. Even with the training from one tracer on one scanner, the effectiveness and robustness of our proposed approach are confirmed in tests of various external imaging tracers on different scanners. The robust, generalizable, and transparent DL development may enhance the potential of clinical translation.
A pathway for chitin oxidation in marine bacteria
Authors: Jiang Wen-Xin , Li Ping-Yi , Chen Xiu-Lan , Zhang Yi-Shuo , Wang Jing-Ping , Wang Yan-Jun , Sheng Qi , Sun Zhong-Zhi , Qin Qi-Long , Ren Xue-Bing , Wang Peng , Song Xiao-Yan , Chen Yin , Zhang Yu-Zhong 
Published: October 2022

AbstractOxidative degradation of chitin, initiated by lytic polysaccharide monooxygenases (LPMOs), contributes to microbial bioconversion of crystalline chitin, the second most abundant biopolymer in nature. However, our knowledge of oxidative chitin utilization pathways, beyond LPMOs, is very limited. Here, we describe a complete pathway for oxidative chitin degradation and its regulation in a marine bacterium, Pseudoalteromonas prydzensis. The pathway starts with LPMO-mediated extracellular breakdown of chitin into C1-oxidized chitooligosaccharides, which carry a terminal 2-(acetylamino)−2-deoxy-D-gluconic acid (GlcNAc1A). Transmembrane transport of oxidized chitooligosaccharides is followed by their hydrolysis in the periplasm, releasing GlcNAc1A, which is catabolized in the cytoplasm. This pathway differs from the known hydrolytic chitin utilization pathway in enzymes, transporters and regulators. In particular, GlcNAc1A is converted to 2-keto-3-deoxygluconate 6-phosphate, acetate and NH3 via a series of reactions resembling the degradation of D-amino acids rather than other monosaccharides. Furthermore, genomic and metagenomic analyses suggest that the chitin oxidative utilization pathway may be prevalent in marine Gammaproteobacteria.
RNA export through the nuclear pore complex is directional
Authors: Ashkenazy-Titelman Asaf , Atrash Mohammad Khaled , Boocholez Alon , Kinor Noa , Shav-Tal Yaron 
Published: October 2022

AbstractThe changes occurring in mRNA organization during nucleo-cytoplasmic transport and export, are not well understood. Moreover, directionality of mRNA passage through the nuclear pore complex (NPC) has not been examined within individual NPCs. Here we find that an mRNP is compact during nucleoplasmic travels compared to a more open structure after transcription and at the nuclear periphery. Compaction levels of nuclear transcripts can be modulated by varying levels of SR proteins and by changing genome organization. Nuclear mRNPs are mostly rod-shaped with distant 5'/3'-ends, although for some, the ends are in proximity. The latter is more abundant in the cytoplasm and can be modified by translation inhibition. mRNAs and lncRNAs exiting the NPC exhibit predominant 5’-first export. In some cases, several adjacent NPCs are engaged in export of the same mRNA suggesting 'gene gating'. Altogether, we show that the mRNP is a flexible structure during travels, with 5'-directionality during export.
Loss of Zfp335 triggers cGAS/STING-dependent apoptosis of post-β selection thymocytes
Authors: Ratiu Jeremy J. , Barclay William E. , Lin Elliot , Wang Qun , Wellford Sebastian , Mehta Naren , Harnois Melissa J. , DiPalma Devon , Roy Sumedha , Contreras Alejandra V. , Shinohara Mari L. , Wiest David , Zhuang Yuan 
Published: October 2022

AbstractProduction of a functional peripheral T cell compartment typically involves massive expansion of the bone marrow progenitors that seed the thymus. There are two main phases of expansion during T cell development, following T lineage commitment of double-negative (DN) 2 cells and after successful rearrangement and selection for functional TCRβ chains in DN3 thymocytes, which promotes the transition of DN4 cells to the DP stage. The signals driving the expansion of DN2 thymocytes are well studied. However, factors regulating the proliferation and survival of DN4 cells remain poorly understood. Here, we uncover an unexpected link between the transcription factor Zfp335 and control of cGAS/STING-dependent cell death in post-β-selection DN4 thymocytes. Zfp335 controls survival by sustaining expression of Ankle2, which suppresses cGAS/STING-dependent cell death. Together, this study identifies Zfp335 as a key transcription factor regulating the survival of proliferating post-β-selection thymocytes and demonstrates a key role for the cGAS/STING pathway in driving apoptosis of developing T cells.
Prion-like low complexity regions enable avid virus-host interactions during HIV-1 infection
Authors: Wei Guochao , Iqbal Naseer , Courouble Valentine V. , Francis Ashwanth C. , Singh Parmit K. , Hudait Arpa , Annamalai Arun S. , Bester Stephanie , Huang Szu-Wei , Shkriabai Nikoloz , Briganti Lorenzo , Haney Reed , KewalRamani Vineet N. , Voth Gregory A. , Engelman Alan N. , Melikyan Gregory B. , Griffin Patrick R. , Asturias Francisco , Kvaratskhelia Mamuka 
Published: October 2022

AbstractCellular proteins CPSF6, NUP153 and SEC24C play crucial roles in HIV-1 infection. While weak interactions of short phenylalanine-glycine (FG) containing peptides with isolated capsid hexamers have been characterized, how these cellular factors functionally engage with biologically relevant mature HIV-1 capsid lattices is unknown. Here we show that prion-like low complexity regions (LCRs) enable avid CPSF6, NUP153 and SEC24C binding to capsid lattices. Structural studies revealed that multivalent CPSF6 assembly is mediated by LCR-LCR interactions, which are templated by binding of CPSF6 FG peptides to a subset of hydrophobic capsid pockets positioned along adjoining hexamers. In infected cells, avid CPSF6 LCR-mediated binding to HIV-1 cores is essential for functional virus-host interactions. The investigational drug lenacapavir accesses unoccupied hydrophobic pockets in the complex to potently impair HIV-1 inside the nucleus without displacing the tightly bound cellular cofactor from virus cores. These results establish previously undescribed mechanisms of virus-host interactions and antiviral action.
Investigating the effects of absolute humidity and movement on COVID-19 seasonality in the United States
Authors: Lin Gary , Hamilton Alisa , Gatalo Oliver , Haghpanah Fardad , Igusa Takeru , Klein Eili 
Published: October 2022

AbstractMounting evidence suggests the primary mode of SARS-CoV-2 transmission is aerosolized transmission from close contact with infected individuals. While transmission is a direct result of human encounters, falling humidity may enhance aerosolized transmission risks similar to other respiratory viruses (e.g., influenza). Using Google COVID-19 Community Mobility Reports, we assessed the relative effects of absolute humidity and changes in individual movement patterns on daily cases while accounting for regional differences in climatological regimes. Our results indicate that increasing humidity was associated with declining cases in the spring and summer of 2020, while decreasing humidity and increase in residential mobility during winter months likely caused increases in COVID-19 cases. The effects of humidity were generally greater in regions with lower humidity levels. Given the possibility that COVID-19 will be endemic, understanding the behavioral and environmental drivers of COVID-19 seasonality in the United States will be paramount as policymakers, healthcare systems, and researchers forecast and plan accordingly.
A study by the lattice discrete element method for exploring the fractal nature of scale effects
Authors: Kosteski Luis Eduardo , Iturrioz Ignacio , Friedrich Leandro Ferreira , Lacidogna Giuseppe 
Published: October 2022

AbstractNowadays, there are many applications in the field of Engineering related to quasi-brittle materials such as ceramics, natural stones, and concrete, among others. When damage is produced, two phenomena can take place: the damage produced governs the collapse process when working with this type of material, and its random nature rules the nonlinear behavior up to the collapse. The interaction among clouds of micro-cracks generates the localization process that implies transforming a continuum domain into a discontinue one. This process also governs the size effect, that is, the changes of the global parameters as the strength and characteristic strain and energies when the size of the structure changes. Some aspects of the scaling law based on the fractal concepts proposed by Prof Carpinteri are analyzed in this work. On the other hand, the Discrete Method is an interesting option to be used in the simulation collapse process of quasi-brittle materials. This method can allow failures with relative ease. Moreover, it can also help to relax the continuum hypothesis. In the present work, a version of the Discrete Element Method is used to simulate the mechanical behavior of different size specimens until collapse by analyzing the size effect represented by this method. This work presents two sets of examples. Its results allow the researchers to see the connection between the numerical results regarding the size effect and the theoretical law based on the fractal dimension of the parameter studied. Two main aspects appear as a result of the analysis presented here. Understand better some aspects of the size effect using the numerical tool and show that the Lattice Discrete Element Method has enough robustness to be applied in the nonlinear analysis of structures built by quasi-brittle materials.
Detecting and mitigating simultaneous waves of COVID-19 infections
Authors: Souyris Sebastian , Hao Shuai , Bose Subhonmesh , England Albert Charles III , Ivanov Anton , Mukherjee Ujjal Kumar , Seshadri Sridhar 
Published: October 2022

AbstractThe sudden spread of COVID-19 infections in a region can catch its healthcare system by surprise. Can one anticipate such a spread and allow healthcare administrators to prepare for a surge a priori? We posit that the answer lies in distinguishing between two types of waves in epidemic dynamics. The first kind resembles a spatio-temporal diffusion pattern. Its gradual spread allows administrators to marshal resources to combat the epidemic. The second kind is caused by super-spreader events, which provide shocks to the disease propagation dynamics. Such shocks simultaneously affect a large geographical region and leave little time for the healthcare system to respond. We use time-series analysis and epidemiological model estimation to detect and react to such simultaneous waves using COVID-19 data from the time when the B.1.617.2 (Delta) variant of the SARS-CoV-2 virus dominated the spread. We first analyze India’s second wave from April to May 2021 that overwhelmed the Indian healthcare system. Then, we analyze data of COVID-19 infections in the United States (US) and countries with a high and low Indian diaspora. We identify the Kumbh Mela festival as the likely super-spreader event, the exogenous shock, behind India’s second wave. We show that a multi-area compartmental epidemiological model does not fit such shock-induced disease dynamics well, in contrast to its performance with diffusion-type spread. The insufficient fit to infection data can be detected in the early stages of a shock-wave propagation and can be used as an early warning sign, providing valuable time for a planned healthcare response. Our analysis of COVID-19 infections in the US reveals that simultaneous waves due to super-spreader events in one country (India) can lead to simultaneous waves in other places. The US wave in the summer of 2021 does not fit a diffusion pattern either. We postulate that international travels from India may have caused this wave. To support that hypothesis, we demonstrate that countries with a high Indian diaspora exhibit infection growth soon after India’s second wave, compared to countries with a low Indian diaspora. Based on our data analysis, we provide concrete policy recommendations at various stages of a simultaneous wave, including how to avoid it, how to detect it quickly after a potential super-spreader event occurs, and how to proactively contain its spread.
Test–retest reliability of upper limb robotic exoskeleton assessments in children and youths with brain lesions
Authors: Graser Judith V. , Prospero Laura , Liesch Monica , Keller Urs , van Hedel Hubertus J. A. 
Published: October 2022

AbstractIn children with congenital or acquired brain lesions, impaired upper limb function can affect independence. Assessing upper limb function is important for planning and evaluating neurorehabilitative interventions. Robotic devices increase measurement-objectivity and enable measuring parameters reflecting more complex motor functions. We investigated the relative and absolute test–retest reliability of assessments to measure upper limb functions in children and adolescents with brain lesions with the exoskeleton ChARMin. Thirty children (9 females, mean age ± SD = 12.5 ± 3.3 years) with congenital brain injuries (n = 15), acquired (n = 14), both (n = 1) and impaired upper limb function participated. They performed the following ChARMin assessments and repeated them within three to seven days: active and passive Range of Motion (ROM), Strength, Resistance to Passive Movement, Quality of Movement, Circle, and Workspace. We calculated the systematic difference, Intraclass Correlation Coefficient (ICC) and Smallest Real Difference (SRD) for each parameter. Six parameters of three assessments showed systematic errors. ICCs ranged from little to very high and SRD values varied considerably. Test–retest reliability and measurement errors ranged widely between the assessments. Systematic differences indicated that random day-to-day variability in performance would be responsible for reduced reliability of those parameters. While it remains debatable whether robot-derived outcomes should replace certain routine assessments (e.g., ROM, strength), we recommend applying certain technology-based assessments also in clinical practice.Trial registration: This study was registered prospectively at ClinicalTrials.gov (identifier: NCT02443857) on May 14, 2015.
Cholecystectomy reduces the risk of myocardial and cerebral infarction in patients with gallstone-related infection
Authors: Park Seon Mee , Kim Hyun Jung , Kang Tae Uk , Swan Heather , Ahn Hyeong Sik 
Published: October 2022

AbstractWe compared the risk of myocardial infarction (MI) or cerebral infarction (CI) in patients with or without-gallstone-related infection (GSI) and change in the risk following cholecystectomy. GSI (n = 84,467) and non-GSI (n = 406,800) patients with age- and sex-matched controls (n = 4,912,670) were identified from Korean population based data. The adjusted hazard ratios (aHRs) of MI or CI were analyzed in both groups treated with or without cholecystectomy. Subgroup analysis was performed for both sexes and different ages. The risk of MI or CI was higher in the GSI group than in the non-GSI group (aHR for MI; 1.32 vs. 1.07, aHR for CI; 1.24 vs. 1.06, respectively). The risk reduction rate of MI following cholecystectomy was 11.4% in the GSI group, whereas it was 0% in the non-GSI group. The risk of CI after cholecystectomy was more reduced in the GSI group than in the non-GSI group (16.1% and 4.7%, respectively). The original risk of MI or CI in patients with gallstones and risk reduction rates following cholecystectomy were higher in females and younger patients than in males and older patients. Increased risk of MI or CI and greater risk reduction following cholecystectomy were seen in patients with GSI.
Production of biodiesel from non-edible feedstocks using environment friendly nano-magnetic Fe/SnO catalyst
Authors: Hanif Maryam , Bhatti Ijaz Ahmad , Zahid Muhammad , Shahid Muhammad 
Published: October 2022

AbstractEnvironmental problems associated with chemical catalysts to fulfil an ever-increasing energy demand have led to the search for an alternative environment friendly heterogeneous catalyst. If a catalyst being used in the biodiesel production is not environment friendly, then the environment is being contaminated in another way while trying to avoid pollution caused by burning of fossil fuels. The present study reports the use of nano-magnetic catalyst Fe/SnO supported on feldspar for the transesterification of various non-edible feedstocks oil, including Pongamiapinnata (karanja), Carthamusoxyacantha (wild safflower), Citrulluscolocynthis (bitter apple), Sinapisarvensis (wildmustard) and Ricinuscommunis (castor). The optimized transesterification parameter was oil to methanol ratio (1:5, 1:10, 1:15, 1:20 and 1:25), catalyst amount (0.5, 1, 1.5, 2, 2.5%), temperature (40, 50, 60, 70 and 80 °C), and reaction times (30, 60, 90, 120 and 150 min). The biodiesel yield was found to be more than 97% for all the tested feedstocks with a maximum biodiesel yield of 98.1 ± 0.6% obtained for bitter apple seed oil under optimum conditions (oil to methanol ratio of 1:10, catalyst amount of 1% at 50 °C for 120 min). The catalysts used for transesterification were magnetically extracted after completion of the reaction. Different physico-chemical parameters like pour point, density, cloud point, iodine value, acid value, saponification and cetane number were determined and the quality of all the biodiesel samples were found to be in the standard range (ASTM D6751 and EN 1404). Different techniques like XRD, FTIR, SEM and EDX were used to characterize the prepared nano-magnetic (Fe/SnO/Feldspar) catalyst.
Global human-edible nutrient supplies, their sources, and correlations with agricultural environmental impact
Authors: White R. R. , Gleason C. B. 
Published: October 2022

AbstractFood production, sustainable development, population growth, and agricultural environmental impacts are linked global problems that require complex solutions. Many efforts evaluating these challenges primarily evaluate dietary strategies designed for health and environmental objectives without considering the subsequent adaptations required by the global food supply. Here we use a complementary approach to summarize trends and variability in the current agricultural system in the context of the growing population and impending environmental challenges. Globally, agricultural systems produce sufficient nutrients to feed 10 billion people with the exception of Ca, DHA + EPA, vitamins B4, D, and E. In a network analysis, greenhouse gas emissions were conditionally dependent on ruminant meat and milk, while water use was conditionally dependent on vegetable and fruit production; however, supplies of most nutrients were also dependent on these same production categories, suggesting trade-offs between nutritional and environmental objectives. Future work should evaluate strategies to address these compromises (i.e., improving water use efficiency and reducing greenhouse gas emissions), to explore to what extent such compromises are biophysically essential or merely a product of the current agricultural system structures. Given the time-sensitive nature of population growth and environmental concerns, strategies to make more effective use of currently produced agricultural products will also be critical complementary strategies to sustainably feed the growing population which can work in concert with other agricultural-, diet- and policy-focused efforts.
Guiding principle of reservoir computing based on “small-world” network
Authors: Kitayama Ken-ichi 
Published: October 2022

AbstractReservoir computing is a computational framework of recurrent neural networks and is gaining attentions because of its drastically simplified training process. For a given task to solve, however, the methodology has not yet been established how to construct an optimal reservoir. While, “small-world” network has been known to represent networks in real-world such as biological systems and social community. This network is categorized amongst those that are completely regular and totally disordered, and it is characterized by highly-clustered nodes with a short path length. This study aims at providing a guiding principle of systematic synthesis of desired reservoirs by taking advantage of controllable parameters of the small-world network. We will validate the methodology using two different types of benchmark tests—classification task and prediction task.