bluuebunny/crossref_metadata_2025 huggingface dataset:
Allergen immunotherapy in house dust mite-associated allergic rhinitis: efficacy of the 300 IR mite tablet
Authors: Klimek Ludger , Brehler Randolf , Casper Ingrid , Klimek Felix , Hagemann Jan , Cuevas Mandy , Bergmann Karl-Christian
Published: January 2023

Background

A perennial house dust mite-associated allergic rhinitis has a major impact on the quality of life of patients and is associated with a high socioeconomic burden. The most common symptoms of allergic rhinitis include a runny nose and nasal congestion, sneezing, itching of nose, mouth and/or throat, and/or ocular symptoms. Affected patients often develop allergic bronchial asthma. Therapy options for allergic rhinitis include allergen avoidance, symptomatic treatment, and allergen immunotherapy. Allergen immunotherapy is the only disease-modifying treatment that can permanently alleviate the symptoms of allergic rhinitis. In July 2021, a new sublingual mite tablet was approved in Germany.

Methods

This review summarizes clinical studies on the 300 IR (index of reactivity) mite tablet in adolescents and adults with house dust mite-associated allergic rhinitis and presents the results.

Results

In the phase II and phase III studies considered here, different dosages of the mite tablet were investigated. The 300 IR mite tablet showed the best benefit–risk profile and has been approved in Europe, Japan, South Korea, Australia, and New Zealand for the treatment of house dust mite-associated allergic rhinitis.

Conclusion

Allergen immunotherapy with the 300 IR mite tablet is an effective treatment that relieves allergic symptoms, reduces the need for symptomatic medication, and improves the quality of life in both adults and adolescents with house dust mite-associated allergic rhinitis. At the same time, treatment with the 300 IR mite tablet is well tolerated. Mild to moderate reactions at the application site subside after a few days.
AC/DC Side Split Capacitor Power Decoupling Circuit
Authors: Liu Peng , Fan Yue , Zhang Yong-gao , Ze Si-yuan
Published: January 2023

Single-phase inverters have a wide range of applications in many fields, but there are inherent double frequency problems, and double frequency fluctuations can easily cause system instability. This paper proposes a mid-point common-mode injection power decoupling circuit. The advantage of this topology is that there are no additional switching devices and only the original DC side support capacitors and filter capacitors of the H-bridge inverter can be used to buffer the double frequency power. The half-bridge structure of this topology enables the AC side capacitors to operate positively and negatively, which can reduce the selection of the withstand voltage of the decoupling capacitor. Simulation and experimental results prove that the method can effectively suppress the secondary ripple on the DC side. The final data shows that the topology can effectively improve the system efficiency after decoupling.
Reflection on feasibility and usability of interactive online international exchange program for occupational therapy students
Authors: Suyama Natsuka , Inoue Kaoru , Sorasak Supatida , Thawisuk Chirathip , Watanabe Masaru
Published: January 2023

The COVID-19 pandemic affected international exchange programs due to travel restrictions. There are few reports of online international exchange programs in medical area and no report of interactive activities among students together for several months. To the best of our knowledge, we needed to seek the feasible approach to conduct online exchange program. We experienced online collaboration works to promote internationalization in occupational therapy (OT) undergraduate education. The aim of this study is to examine the feasibility and usability of an interactive online international exchange program, and discuss its challenges and advantages. The three-month program was newly developed, and aimed at cultivating an international perspective, understanding OT, and learning basic research skills. Students’ interests and the development of their motivation were considered in the program consisting of synchronous and asynchronous lectures, a collaboration research project, group work, and report assignments. Through the program, students were satisfied with the program contents and had the precious experience to develop international relationships. The online exchange program provided students with the opportunity to experience and learn OT education internationally at an economical cost, and to achieve program goal during the regular semester. In this program, students not only acquired knowledge in their professional field, but also cultivated their international communication skills in English from small group activities and social activities. Considering various communication methods was an important aspect in the virtual environment leading to a successful program. In medical education, an online program can be an effective and practical measure for international exchange.
The Advantages of Single-Room Management in an ICU and the Changing Trend of Drug-Resistant Bacteria over the Last 5 Years
Authors: Wang Ru , Xia Jing , Zhao Shibing
Published: January 2023

Objective

We reviewed the benefits of an all-single-room intensive care unit in the prevention of hospital-acquired infection.

Method

The intensive care medicine department of the First Affiliated Hospital of Bengbu Medical College commenced single-room management in 2019. This study reviewed the prevalence of pathogenic bacterial infection and altered drug resistance of major pathogens in patients hospitalized from January 2016 to December 2020. Results of bacterial resistance and changes in bacterial numbers were analyzed separately and the two time periods compared.

Results

In 2016, 320 strains of pathogenic bacteria were identified compared with 601 in 2020. At both times, bacteria were predominantly gram-negative. The ratio of the number of pathogenic bacteria to the number of beds revealed a decreasing trend each year from 2016–2020: 22.86, 17.57, 28.36, 14.33, and 15.41 respectively (P < 0.05). The top five Gram-negative bacteria were Acinetobacter baumannii, Klebsiella pneumoniae, Pseudomonas aeruginosa, Escherichia coli, and Burkholderia cepacia. The source of bacteria was mainly sputum, followed by blood, and the site of infection was predominantly the respiratory tract. Staphylococcus aureus resistant to ciprofloxacin, levofloxacin and erythromycin had decreased significantly (P < 0.05). Among the multi-drug resistant bacteria detected, only penicillin-resistant Klebsiella pneumoniae and penicillin-resistant Pseudomonas aeruginosa decreased after the introduction of single-room wards (P = 0.025, P = 0.002 respectively).

Conclusion

Introduction of a single-room ward directly or indirectly reduced the possibility of cross-infection. The establishment of single-room wards has no adverse effects and was beneficial to patients, the department and the hospital.
Improvement of FFD parametric approach in the application of a lifting body
Authors: Leng J.-x. , Wang Z.-g. , Huang W. , Shen Y. , An K.
Published: January 2023

FFD (free-form deformation method) is one of the most commonly used parameterisation methods at present. It places the parameterised objects inside the control volume through coordinate system transformation, and controls the control volume through control points, thus realising the deformation control of its internal objects. Firstly, this paper systematically analyses and compares the characteristics and technical requirements of Bernstein, B-spline and NURBS (non-uniform rational b-splines) basic functions that can be adopted by FFD, and uses the minimum number of control points required to achieve the specified control effect threshold to express the control capability. Aiming at the problem of discontinuity at the right end in the actual calculation of B-spline basis function, a method of adding a small epsilon is proposed to solve it. Then, three basic functions are applied to the FFD parameterisation method, respectively, and the differences are compared from two aspects of the accurate expression of the model and the ability of deformation control. It is found that the BFFD (b-spline free-form deformation) approach owns better comprehensive performance when the control points are distributed correctly. In this paper, the BFFD method is improved, and a p-BFFD (reverse solution points based BFFD) method based on inverse solution is proposed to realise the free distribution of control points under the specified topology. Further, for the lifting body configuration, the control points of the p-BFFD method are brought closer to the airframe forming the EDGE-p-BFFD (edge constraints based p-BFFD) method. For the case in this paper, the proposed EDGE-p-BFFD method not only has fairly high parameterisation accuracy, but also reduces the expression error from 1.01E-3 to 1.25E-4, which is nearly ten times. It can also achieve effective lifting body guideline constraints, and has the ability of local deformation adapting to the configuration characteristics. In terms of the proportion of effective control points, the EDGE-p-BFFD method increases the proportion of effective control points from 36.7% to 50%, and the more control points, the more obvious the proportion increase effect. The new method also has better effect on the continuity of geometric deformation. At the same time, this paper introduces the independent deformation method of the upper and lower surfaces based on the double control body frames, which effectively avoids the deformation coupling problem of the simultaneous change of the upper and lower surfaces caused by the movement of control points in the traditional single control framework.
Population development as a driver of coastal risk: Current trends and future pathways
Authors: Reimann Lena , Vafeidis Athanasios T. , Honsel Lars E.
Published: January 2023

Coastal areas are subject to hazards that can result in severe impacts due to the high concentration of people and assets in exposed locations. While climate-induced sea-level rise will exacerbate these hazards in the course of the 21st century, future dynamics in socioeconomic development will play an important role in driving impacts – as well as adaptation responses – in particular in countries with rapid population growth in low-lying coastal areas. Here, we synthesize the current state of knowledge related to current and future population development in coastal locations and the underlying trends in socioeconomic development affecting coastal impacts at continental to global scales. Currently, 2.15 billion people live in the near-coastal zone and 898 million in the low-elevation coastal zone globally. These numbers could increase to 2.9 billion and 1.2 billion, respectively, depending on the socioeconomic scenario (i.e., Shared Socioeconomic Pathway [SSP]) considered. Nevertheless, although these numbers indicate a rapid increase in exposure of population and assets to coastal hazards, they bear limited information about the actual impacts as they do not include information on the vulnerability of coastal population. Based on these insights, we stress the need to account for dynamics in socioeconomic development in coastal risk assessments, including exposure as well as vulnerability, and additionally exploring potential feedbacks due to adaptation responses and migration decisions. Last, we propose action points for future work that can inform long-term coastal planning for managing coastal risks.
Real-time flow measurement system: physics-informed reconstruction and sampling strategy
Authors: Humml Julian , Schaufelberger Frank , Rösgen Thomas , Meyer Daniel W.
Published: January 2023

In this work, we focus on a multi-hole pressure-probe-based flow measurement system for wind tunnel measurements that provides real-time feedback to a robot probe-manipulator, rendering the system autonomous. The system relies on a novel, computationally efficient flow analysis technique that translates the probe's point measurements of velocity and pressure into an updatable mean flow map that is accompanied by an uncertainty metric. The latter provides guidance to the manipulator when planning the optimal probe path. The probe is then guided by the robot in the flow domain until an available time budget has been exhausted, or until the uncertainty metric falls below a prescribed target threshold in the entire flow domain. We assess the capabilities of our new measurement system using computational fluid dynamics data, for which the ground truth is available in the form of a mean flow field. An application in a real wind tunnel setting is provided as well.
Effect of aspect ratio on the propulsive performance of tandem flapping foils
Authors: Lagopoulos N. S. , Weymouth G. D. , Ganapathisubramani B.
Published: January 2023

In this work, we describe the impact of aspect ratio ($AR$) on the performance of optimally phased, identical flapping flippers in a tandem configuration. Three-dimensional simulations are performed for seven sets of single and tandem finite foils at a moderate Reynolds number, with thrust producing, heave-to-pitch coupled kinematics. Increasing slenderness (or$AR$) is found to improve thrust coefficients and thrust augmentation but the benefits level off towards higher values of$AR$. However, the propulsive efficiency shows no significant change with increasing$AR$, while the hind foil outperforms the single by a small margin. Further analysis of the spanwise development and propagation of vortical structures allows us to gain some insights into the mechanisms of these wake interactions and provide valuable information for the design of novel biomimetic propulsion systems.
Reciprocal properties of random fields on undirected graphs
Authors: Erhardsson Torkel
Published: January 2023

We clarify and refine the definition of a reciprocal random field on an undirected graph, with the reciprocal chain as a special case, by introducing four new properties: the factorizing, global, local, and pairwise reciprocal properties, in decreasing order of strength, with respect to a set of nodes
$\delta$
. They reduce to the better-known Markov properties if
$\delta$
is the empty set, or, with the exception of the local property, if
$\delta$
is a complete set. Conditions for each reciprocal property to imply the next stronger property are derived, and it is shown that, conditionally on the values at a set of nodes
$\delta_0$
, all four properties are preserved for the subgraph induced by the remaining nodes, with respect to the node set
$\delta\setminus\delta_0$
. We note that many of the above results are new even for reciprocal chains.
Effect of a fishing closure on Chamelea gallina stocks along the Turkish coast
Authors: Dağtekin Murat , Dalgıç Göktuğ , Erbay Murat , Özcan Akpinar İlkay , Aydın Mehmet , Özdemir Süleyman , Karayücel Sedat , Özyurt Caner Enver
Published: January 2023

The striped venus clam Chamelea gallina (SVE), plays an important role as an infaunal filter-feeder in the ecosystem, besides an important economic role in the Black Sea coasts of Turkey. It is caught using hydraulic dredge boats, then processed, and the final product (frozen meat) is exported to EU countries. SVE fishing requires a special licence and regulations. Also, SVE beds were closed to fisheries for the recovery of stocks for 2 years. In the study, SVE beds were investigated during the closed season over two years to assess stock density. Additionally, the number of macrobenthic species that share the same habitat as the SVE was determined. The sampling area was divided into five sub-areas and four strata by depth and then stratified random sampling was applied to collect data. In 2011, SVE stock sizes in the sub-areas were 11,723.58 ± 5167.262 tons (Cide), 35,082.94 ± 27,510.95 tons (İnebolu), 10,077.05 ± 4970.68 tons (Türkeli), 3304.36 ± 3215.1 tons (Ayancık) and 1431.3 ± 1703.5 tons (Sarıkum). In 2012, these estimated stocks were 13,820.41 ± 6977.86 tons, 34,841.94 ± 14,623.71 tons, 8148.27 ± 5006.74 tons, 3420.72 ± 3093.67 tons and 2023.74 ± 2832.63 tons, respectively. However, the estimated SVE total biomass did not change significantly during the period when the fields were closed (P > 0.05). The results indicate that length-weight relationship parameters varied of b from 2.9011–2.9072 in two years. Shell damage during fishing, environmental factors, food competition and consumption by the main predator all have a significant impact on stock densities, and changes occurring in these conditions should be considered in fisheries management.
Accidental Scientists: How Undergraduate Research in Political Science Can Help to Patch the “Leaky Pipeline” in STEM Education
Authors: Mueller Lisa
Published: January 2023

Education advocates lament the “leaky pipeline” in science, technology, engineering, and math (STEM), whereby students—especially minorities and women—drop out of STEM at successive stages of the educational system. Defining empirical political science as a branch of STEM, this article proposes that undergraduate research in political science can help to patch this leaky pipeline and expand access to scientific skills and habits of mind. I elaborate on three rationales to support my claim: (1) political science is a relatively diverse field of STEM; (2) college primes students to think like (political) scientists; and (3) students often encounter political science research opportunities for the first time as undergraduates, presenting an opportunity for faculty to “catch” those who selected out of STEM after high school. I substantiate my arguments by drawing on enrollment data, archival documents, the theories of John Dewey, and testimonials from former undergraduate researchers. I also recommend ways for political science departments to provide a meaningful STEM education by enhancing research programs.
Health misinformation and freedom of expression: considerations for policymakers
Authors: Marecos João , Shattock Ethan , Bartlett Oliver , Goiana-da-Silva Francisco , Maheswaran Hendramoorthy , Ashrafian Hutan , Darzi Ara
Published: January 2023

Health misinformation, most visibly following the COVID-19 infodemic, is an urgent threat that hinders the success of public health policies. It likely contributed, and will continue to contribute, to avoidable deaths. Policymakers around the world are being pushed to tackle this problem. Legislative acts have been rolled out or announced in many countries and at the European Union level. The goal of this paper is not to review particular legislative initiatives, or to assess the impact and efficacy of measures implemented by digital intermediaries, but to reflect on the high constitutional and ethical stakes involved in tackling health misinformation through speech regulation. Our findings suggest that solutions focused on regulating speech are likely to encounter significant constraints, as policymakers grasp with the limitations imposed by freedom of expression and ethical considerations. Solutions focused on empowering individuals – such as media literacy initiatives, fact-checking or credibility labels – are one way to avoid such hurdles.
In‐Flight Calibration of Near‐Infrared Reflectance Spectra Measured by the Zhurong Mars Rover
Authors: Lin Honglei , Xu Rui , Lin Yangting , Xu Xuesen , Wu Bing , Gou Sheng , Wei Yong
Published: January 2023

The Zhurong rover of the China's first Mars Exploration Mission successfully landed on the northern plain of Mars and measured near‐infrared (NIR) reflectance spectra with the Mars Surface Composition Detector (MarSCoDe). There was only orbital NIR hyperspectral data before the success of the Zhurong and Perseverance rovers in 2021. The in situ spectral measurements by the rover face different problems when compared with orbital measurements in data analysis, and thus need a new process pipeline. We analyzed the factors affecting the quality of the NIR spectra acquired by the Zhurong rover, including temperature variation of the detector, non‐homogeneous properties of the calibration panels, the atmosphere transmission and Martian dust buildup on the calibration panels. We then identified that the Martian dust buildup on the calibration panels is the main factor affecting the spectra, causing significant discrepancies between the reflectance calibrated with the white and gray panels, respectively, and the systematically higher reflectance values of the Martian soils measured by the Zhurong rover than those by other missions. We proposed a spectral unmixing strategy to restore the radiance of clean calibration panels on the rover and then derived the reflectance spectra with an uncertainty of ∼14%. The method has been tested by simulation experiments in laboratory. The data quality of the in situ NIR spectra of the Zhurong rover is significantly improved after the calibrations based on our pipeline, which is critical for mineral identification on small scales and calibrations of the orbital remote sensing data.
Fluvial and Marine Depositional Environments Determined From Groundwater Chemistry and Calculated Clay‐Cation Compositions
Authors: Jones Cole R. , Capuano Regina M.
Published: January 2023

Cation mole precents (XCa, XMg, and XNa) on clay minerals in a siliciclastic coastal aquifer calculated from groundwater compositions, can aid in distinguishing fluvial from marine sediments and locate the fluvial/marine transition zone. The clay‐cation compositions of two clay‐rich siliciclastic coastal aquifers calculated from the composition of the groundwater were compared to the location of fluvial, fluvial‐marine transition and marine environments identified by traditional core, well log and paleontological analyses. The traditionally defined fluvial depositional environment is distinguished by clays with low XNa < 8% (for 92% of the samples) and high XCa from 55% to 98% with the remainder XMg. In comparison, the traditionally defined marine depositional environment is distinguished by clays with higher XNa > 8.0% (for 86% of the samples) and lower XCa ranging from 5% to 39% with the remainder XMg. The traditionally defined fluvial/marine transition zone has values overlapping the fluvial and marine end members, with 59% with XNa < 8% (fluvial) and 41% with XNa > 8% (marine), and XCa ranging from 45% to 98% with the remainder XMg. Calculations support that the excess Na (XNa > 8%) on marine clays can be retained for 10s of millions of years despite flushing with meteoric water, because of the high clay content in marine sediments. The calculated cation composition of clays deposited from river water are XNa < 8%. In contrast XNa 8%–54% is possible for seawater equilibrated clays supporting that the values found in the different depositional zones are possible. Calculated cation compositions might supplement traditional stratigraphic interpretations in distinguishing fluvial/marine depositional environments.
Single-molecule visualization of mRNA circularization during translation
Authors: Kim Byungju , Seol Jincheol , Kim Yoon Ki , Lee Jong-Bong
Published: January 2023

Translation is mediated by precisely orchestrated sequential interactions among translation initiation components, mRNA, and ribosomes. Biochemical, structural, and genetic techniques have revealed the fundamental mechanism that determines what occurs and when, where and in what order. Most mRNAs are circularized via the eIF4E–eIF4G–PABP interaction, which stabilizes mRNAs and enhances translation by recycling ribosomes. However, studies using single-molecule fluorescence imaging have allowed for the visualization of complex data that opposes the traditional “functional circularization” theory. Here, we briefly introduce single-molecule techniques applied to studies on mRNA circularization and describe the results of in vitro and live-cell imaging. Finally, we discuss relevant insights and questions gained from single-molecule research related to translation.
White matter lesion load determines exercise-induced dopaminergic plasticity and working memory gains in aging
Authors: von Cederwald Bryn Farnsworth , Johansson Jarkko , Riklund Katrine , Karalija Nina , Boraxbekk Carl-Johan
Published: January 2023

Age-related dopamine reductions have been suggested to contribute to maladaptive working memory (WM) function in older ages. One promising intervention approach is to increase physical activity, as this has been associated with plasticity of the striatal dopamine system and WM improvements, however with individual differences in efficacy. The present work focused on the impact of individual differences in white-matter lesion burden upon dopamine D2-like receptor (DRD2) availability and WM changes in response to a 6 months physical activity intervention. While the intervention altered striatal DRD2 availability and WM performance in individuals with no or only mild lesions (p < 0.05), no such effects were found in individuals with moderate-to-severe lesion severity (p > 0.05). Follow-up analyses revealed a similar pattern for processing speed, but not for episodic memory performance. Linear analyses further revealed that lesion volume (ml) at baseline was associated with reduced DRD2 availability (r = −0.41, p < 0.05), and level of DRD2 change (r = 0.40, p < 0.05). Taken together, this study underlines the necessity to consider cerebrovascular health in interventions with neurocognitive targets. Future work should assess whether these findings extend beyond measures of DRD2 availability and WM.
Human zygotic genome activation is initiated from paternal genome
Authors: Yuan Shenli , Zhan Jianhong , Zhang Jingye , Liu Zhenbo , Hou Zhenzhen , Zhang Chuanxin , Yi Lizhi , Gao Lei , Zhao Han , Chen Zi-Jiang , Liu Jiang , Wu Keliang
Published: January 2023

Although parental genomes undergo extensive epigenetic reprogramming to be equalized after fertilization, whether they play different roles in human zygotic genome activation (ZGA) remains unknown. Here, we mapped parental transcriptomes by using human parthenogenetic (PG) and androgenetic (AG) embryos during ZGA. Our data show that human ZGA is launched at the 8-cell stage in AG and bi-parental embryos, but at the morula stage in PG embryos. In contrast, mouse ZGA occurs at the same stage in PG and AG embryos. Mechanistically, primate-specific ZNF675 with AG-specific expression plays a role in human ZGA initiated from paternal genome at the 8-cell stage. AG-specifically expressed LSM1 is also critical for human maternal RNA degradation (MRD) and ZGA. The allelic expressions of ZNF675 and LSM1 are associated with their allelically epigenetic states. Notably, the paternally specific expressions of ZNF675 and LSM1 are also observed in diploid embryos. Collectively, human ZGA is initiated from paternal genome.
Correlated evolution of social organization and lifespan in mammals
Authors: Zhu Pingfen , Liu Weiqiang , Zhang Xiaoxiao , Li Meng , Liu Gaoming , Yu Yang , Li Zihao , Li Xuanjing , Du Juan , Wang Xiao , Grueter Cyril C. , Li Ming , Zhou Xuming
Published: January 2023

Discerning the relationship between sociality and longevity would permit a deeper understanding of how animal life history evolved. Here, we perform a phylogenetic comparative analysis of ~1000 mammalian species on three states of social organization (solitary, pair-living, and group-living) and longevity. We show that group-living species generally live longer than solitary species, and that the transition rate from a short-lived state to a long-lived state is higher in group-living than non-group-living species, altogether supporting the correlated evolution of social organization and longevity. The comparative brain transcriptomes of 94 mammalian species identify 31 genes, hormones and immunity-related pathways broadly involved in the association between social organization and longevity. Further selection features reveal twenty overlapping pathways under selection for both social organization and longevity. These results underscore a molecular basis for the influence of the social organization on longevity.
Spatially resolved transcriptomic profiling of degraded and challenging fresh frozen samples
Authors: Mirzazadeh Reza , Andrusivova Zaneta , Larsson Ludvig , Newton Phillip T. , Galicia Leire Alonso , Abalo Xesús M. , Avijgan Mahtab , Kvastad Linda , Denadai-Souza Alexandre , Stakenborg Nathalie , Firsova Alexandra B. , Shamikh Alia , Jurek Aleksandra , Schultz Niklas , Nistér Monica , Samakovlis Christos , Boeckxstaens Guy , Lundeberg Joakim
Published: January 2023

Spatially resolved transcriptomics has enabled precise genome-wide mRNA expression profiling within tissue sections. The performance of methods targeting the polyA tails of mRNA relies on the availability of specimens with high RNA quality. Moreover, the high cost of currently available spatial resolved transcriptomics assays requires a careful sample screening process to increase the chance of obtaining high-quality data. Indeed, the upfront analysis of RNA quality can show considerable variability due to sample handling, storage, and/or intrinsic factors. We present RNA-Rescue Spatial Transcriptomics (RRST), a workflow designed to improve mRNA recovery from fresh frozen specimens with moderate to low RNA quality. First, we provide a benchmark of RRST against the standard Visium spatial gene expression protocol on high RNA quality samples represented by mouse brain and prostate cancer samples. Then, we test the RRST protocol on tissue sections collected from five challenging tissue types, including human lung, colon, small intestine, pediatric brain tumor, and mouse bone/cartilage. In total, we analyze 52 tissue sections and demonstrate that RRST is a versatile, powerful, and reproducible protocol for fresh frozen specimens of different qualities and origins.
Host-microbe co-metabolism via MCAD generates circulating metabolites including hippuric acid
Authors: Pruss Kali M. , Chen Haoqing , Liu Yuanyuan , Van Treuren William , Higginbottom Steven K. , Jarman John B. , Fischer Curt R. , Mak Justin , Wong Beverly , Cowan Tina M. , Fischbach Michael A. , Sonnenburg Justin L. , Dodd Dylan
Published: January 2023

The human gut microbiota produces dozens of small molecules that circulate in blood, accumulate to comparable levels as pharmaceutical drugs, and influence host physiology. Despite the importance of these metabolites to human health and disease, the origin of most microbially-produced molecules and their fate in the host remains largely unknown. Here, we uncover a host-microbe co-metabolic pathway for generation of hippuric acid, one of the most abundant organic acids in mammalian urine. Combining stable isotope tracing with bacterial and host genetics, we demonstrate reduction of phenylalanine to phenylpropionic acid by gut bacteria; the host re-oxidizes phenylpropionic acid involving medium-chain acyl-CoA dehydrogenase (MCAD). Generation of germ-free male and female MCAD−/− mice enabled gnotobiotic colonization combined with untargeted metabolomics to identify additional microbial metabolites processed by MCAD in host circulation. Our findings uncover a host-microbe pathway for the abundant, non-toxic phenylalanine metabolite hippurate and identify β-oxidation via MCAD as a novel mechanism by which mammals metabolize microbiota-derived metabolites.
Mechanism of hormone and allosteric agonist mediated activation of follicle stimulating hormone receptor
Authors: Duan Jia , Xu Peiyu , Zhang Huibing , Luan Xiaodong , Yang Jiaqi , He Xinheng , Mao Chunyou , Shen Dan-Dan , Ji Yujie , Cheng Xi , Jiang Hualiang , Jiang Yi , Zhang Shuyang , Zhang Yan , Xu H. Eric
Published: January 2023

Follicle stimulating hormone (FSH) is an essential glycoprotein hormone for human reproduction, which functions are mediated by a G protein-coupled receptor, FSHR. Aberrant FSH-FSHR signaling causes infertility and ovarian hyperstimulation syndrome. Here we report cryo-EM structures of FSHR in both inactive and active states, with the active structure bound to FSH and an allosteric agonist compound 21 f. The structures of FSHR are similar to other glycoprotein hormone receptors, highlighting a conserved activation mechanism of hormone-induced receptor activation. Compound 21 f formed extensive interactions with the TMD to directly activate FSHR. Importantly, the unique residue H6157.42 in FSHR plays an essential role in determining FSHR selectivity for various allosteric agonists. Together, our structures provide a molecular basis of FSH and small allosteric agonist-mediated FSHR activation, which could inspire the design of FSHR-targeted drugs for the treatment of infertility and controlled ovarian stimulation for in vitro fertilization.
Global vegetation resilience linked to water availability and variability
Authors: Smith Taylor , Boers Niklas
Published: January 2023

Quantifying the resilience of vegetated ecosystems is key to constraining both present-day and future global impacts of anthropogenic climate change. Here we apply both empirical and theoretical resilience metrics to remotely-sensed vegetation data in order to examine the role of water availability and variability in controlling vegetation resilience at the global scale. We find a concise global relationship where vegetation resilience is greater in regions with higher water availability. We also reveal that resilience is lower in regions with more pronounced inter-annual precipitation variability, but find less concise relationships between vegetation resilience and intra-annual precipitation variability. Our results thus imply that the resilience of vegetation responds differently to water deficits at varying time scales. In view of projected increases in precipitation variability, our findings highlight the risk of ecosystem degradation under ongoing climate change.
Epigenetic control of cellular crosstalk defines gastrointestinal organ fate and function
Authors: Smith Ryan J. , Liang Minggao , Loe Adrian Kwan Ho , Yung Theodora , Kim Ji-Eun , Hudson Matthew , Wilson Michael D. , Kim Tae-Hee
Published: January 2023

Epithelial-mesenchymal signaling in the gastrointestinal system is vital in establishing regional identity during organogenesis and maintaining adult stem cell homeostasis. Although recent work has demonstrated that Wnt ligands expressed by mesenchymal cells are required during gastrointestinal development and stem cell homeostasis, epigenetic mechanisms driving spatiotemporal control of crosstalk remain unknown. Here, we demonstrate that gastrointestinal mesenchymal cells control epithelial fate and function through Polycomb Repressive Complex 2-mediated chromatin bivalency. We find that while key lineage-determining genes possess tissue-specific chromatin accessibility, Polycomb Repressive Complex 2 controls Wnt expression in mesenchymal cells without altering accessibility. We show that reduction of mesenchymal Wnt secretion rescues gastrointestinal fate and proliferation defects caused by Polycomb Repressive Complex 2 loss. We demonstrate that mesenchymal Polycomb Repressive Complex 2 also regulates niche signals to maintain stem cell function in the adult intestine. Our results highlight a broadly permissive chromatin architecture underlying regionalization in mesenchymal cells, then demonstrate further how chromatin architecture in niches can influence the fate and function of neighboring cells.
Molecular insights into the gating mechanisms of voltage-gated calcium channel CaV2.3
Authors: Gao Yiwei , Xu Shuai , Cui Xiaoli , Xu Hao , Qiu Yunlong , Wei Yiqing , Dong Yanli , Zhu Boling , Peng Chao , Liu Shiqi , Zhang Xuejun Cai , Sun Jianyuan , Huang Zhuo , Zhao Yan
Published: January 2023

High-voltage-activated R-type CaV2.3 channel plays pivotal roles in many physiological activities and is implicated in epilepsy, convulsions, and other neurodevelopmental impairments. Here, we determine the high-resolution cryo-electron microscopy (cryo-EM) structure of human CaV2.3 in complex with the α2δ1 and β1 subunits. The VSDII is stabilized in the resting state. Electrophysiological experiments elucidate that the VSDII is not required for channel activation, whereas the other VSDs are essential for channel opening. The intracellular gate is blocked by the W-helix. A pre-W-helix adjacent to the W-helix can significantly regulate closed-state inactivation (CSI) by modulating the association and dissociation of the W-helix with the gate. Electrostatic interactions formed between the negatively charged domain on S6II, which is exclusively conserved in the CaV2 family, and nearby regions at the alpha-interacting domain (AID) and S4-S5II helix are identified. Further functional analyses indicate that these interactions are critical for the open-state inactivation (OSI) of CaV2 channels.
Tailored cluster states with high threshold under biased noise
Authors: Claes Jahan , Bourassa J. Eli , Puri Shruti
Published: January 2023

Fault-tolerant cluster states form the basis for scalable measurement-based quantum computation. Recently, new stabilizer codes for scalable circuit-based quantum computation have been introduced that have very high thresholds under biased noise where the qubit predominantly suffers from one type of error, e.g. dephasing. However, extending these advances in stabilizer codes to generate high-threshold cluster states for biased noise has been a challenge, as the standard method for foliating stabilizer codes to generate fault-tolerant cluster states does not preserve the noise bias. In this work, we overcome this barrier by introducing a generalization of the cluster state that allows us to foliate stabilizer codes in a bias-preserving way. As an example of our approach, we construct a foliated version of the XZZX code which we call the XZZX cluster state. We demonstrate that under a circuit-level-noise model, our XZZX cluster state has a threshold more than double the usual cluster state when dephasing errors are more likely than errors that cause bit flips by a factor of order ~100 or more.
Caravan - A global community dataset for large-sample hydrology
Authors: Kratzert Frederik , Nearing Grey , Addor Nans , Erickson Tyler , Gauch Martin , Gilon Oren , Gudmundsson Lukas , Hassidim Avinatan , Klotz Daniel , Nevo Sella , Shalev Guy , Matias Yossi
Published: January 2023

High-quality datasets are essential to support hydrological science and modeling. Several CAMELS (Catchment Attributes and Meteorology for Large-sample Studies) datasets exist for specific countries or regions, however these datasets lack standardization, which makes global studies difficult. This paper introduces a dataset calledCaravan(a series of CAMELS) that standardizes and aggregates seven existing large-sample hydrology datasets. Caravan includes meteorological forcing data, streamflow data, and static catchment attributes (e.g., geophysical, sociological, climatological) for 6830 catchments. Most importantly, Caravan is both a dataset and open-source software that allows members of the hydrology community to extend the dataset to new locations by extracting forcing data and catchment attributes in the cloud. Our vision is for Caravan to democratize the creation and use of globally-standardized large-sample hydrology datasets. Caravan is a truly global open-source community resource.
AerialWaste dataset for landfill discovery in aerial and satellite images
Authors: Torres Rocio Nahime , Fraternali Piero
Published: January 2023

Illegal landfills are sites where garbage is dumped violating waste management laws. Aerial images enable the use of photo interpretation for territory scanning and landfill detection but this practice is hindered by the manual nature of this task which also requires expert knowledge. Deep Learning methods can help capture the analysts’ expertise and build automated landfill discovery tools. However, this goal requires public high-quality datasets for model training and testing. At present no such datasets exist and this gap penalizes the research toward scalable and accurate landfill discovery methods. We present a dataset for landfill detection featuring airborne, WorldView-3, and GoogleEarth images annotated by professional photo interpreters. It comprises 3,478 positive and 6,956 negative examples. Most positive instances are characterized by metadata: the type of waste, its storage mode, the type of the site, and the evidence and severity of the illicit. The dataset has been technically validated by building an accurate landfill detector and is accompanied by a visualization and annotation tool.
Computational analysis of coiled tubing concerns during oil well intervention in the upper Assam basin, India
Authors: Neog Dhrubajyoti , Sarmah Ankur , Baruah Mohammad Irfan Sunny
Published: January 2023

Coil tubing (CT) is widely regarded as one of the most effective servicing tools for dealing with a variety of oil and gas production issues, and it is also commonly used for oil well workover operations in India's upper Assam basin. The current work considers QT 800 to be the CT material used for actual oil well operations. With reference to actual operations carried out in some of the oil wells in the upper Assam basin, the current research analyses the limitations of CTs (QT 800, QT 900, and QT 1000) based on developing limit curves that can depict the operating limit and infer CT failure probability. This study also includes fatigue analysis to determine the likelihood of damage from hot oil circulation, water injection, and nitrogen shot operations while performing them using the CTs (QT 700, QT 800, QT 900, and QT 1000). The current work adopts the methodology of CT assessment based on a computational model built in MATLAB with respect to different oil well parameters in the upper Assam basin. This study takes an innovative approach by taking downhole temperature into account when determining the CT limit for QT 800, which signifies novelty in the current work. According to the computational analysis used in the study on CT limits, mechanical strain, thermal strain, and the combined strain of the CT material all affect CT elongation. This observation was often found to be a research gap in different research works as this aspect in previous studies was not considered while analysing CT operations. The findings of the present study highlight and draw the conclusion that temperature variations in the well and the CTU’s circulating fluid contribute linearly to CT strain. CT’s working limit diminishes with increasing internal and external pressure and diametrical growth, which eventually causes fatigue damage.
Prioritization of thermal energy techniques by employing picture fuzzy soft power average and geometric aggregation operators
Authors: Mahmood Tahir , Ahmmad Jabbar , Gwak Jeonghwan , Jan Naeem
Published: January 2023

Energy storage is a way of storing energy to reduce imbalances between demand and energy production. The ability to store electricity and use it later is one of the keys to reaching large quantities of renewable energy on the grid. There are several methods to store energy such as mechanical, electrical, chemical, electrochemical, and thermal energy. Regarding their operation, storage, and cost, the choice of these energy storage techniques appears to be interesting. This issue becomes very serious when there involves uncertainty. To consider this kind of uncertain information, a picture fuzzy soft set is found to be a more appropriate parameterization tool to deal with imprecise data. Based on the advanced structure of picture fuzzy soft set, here in this article, firstly, we have developed the notions of basic operational laws for picture fuzzy soft numbers. Then based on these developed operational laws, we have established the notions of picture fuzzy soft power average $$\left({\mathrm{PFS}}_{\mathrm{ft}}\mathrm{PA}\right)$$

PFS
ft

PA

, weighted picture fuzzy soft power average $$\left({\mathrm{WPFS}}_{\mathrm{ft}}\mathrm{PA}\right)$$

WPFS
ft

PA

and ordered weighted picture fuzzy soft power average $$\left({\mathrm{OWPFS}}_{\mathrm{ft}}\mathrm{PA}\right)$$

OWPFS
ft

PA

aggregation operators. Moreover, we have introduced the notions for picture fuzzy soft power geometric $$\left({\mathrm{PFS}}_{\mathrm{ft}}\mathrm{PG}\right)$$

PFS
ft

PG

, weighted picture fuzzy soft power geometric $$\left({\mathrm{WPFS}}_{\mathrm{ft}}\mathrm{PG}\right)$$

WPFS
ft

PG

and ordered weighted picture fuzzy soft power geometric $$\left({\mathrm{OWPFS}}_{\mathrm{ft}}\mathrm{PG}\right)$$

OWPFS
ft

PG

aggregation operators. Furthermore, we have established the application of picture fuzzy soft power aggregation operators for the selection of thermal energy storage techniques. For this, we have developed a decision-making approach along with an explanatory example to show the effective use of the developed theory. Furthermore, a comparative analysis of the introduced work shows the advancement of developed notions.
Elevated alpha diversity in disturbed sites obscures regional decline and homogenization of amphibian taxonomic, functional and phylogenetic diversity
Authors: Dehling D. Matthias , Dehling J. Maximilian
Published: January 2023

Loss of natural habitat due to land-use change is one of the major threats to biodiversity worldwide. It not only affects the diversity of local species communities (alpha diversity) but can also lead to large-scale homogenization of community composition (reduced beta diversity) and loss of regional diversity (gamma diversity), but these effects are still rarely investigated. We assessed the impact of land-use change on taxonomic, functional and phylogenetic diversity of amphibians in Rwanda, both on the local (community-level) and regional scale (country-wide). Alpha diversity in local communities was higher in farmland than in natural habitats; however, species turnover among farmland sites was much lower than among natural sites, resulting in highly homogenized communities and reduced taxonomic, functional and phylogenetic gamma diversity in farmland across Rwanda. Amphibians found in farmland were mostly disturbance-tolerant species that are widespread in eastern Africa and beyond. In contrast, most of the regionally endemic frog species that make this region a continent-wide hotspot of amphibian diversity were found only in the natural habitats. Ongoing habitat conversion might result in further homogenization of amphibian communities across sub-Saharan Africa and the loss of regional endemism, unique evolutionary lineages, and multifunctionality.
Knowledge mining of unstructured information: application to cyber domain
Authors: Takko Tuomas , Bhattacharya Kunal , Lehto Martti , Jalasvirta Pertti , Cederberg Aapo , Kaski Kimmo
Published: January 2023

Information on cyber-related crimes, incidents, and conflicts is abundantly available in numerous open online sources. However, processing large volumes and streams of data is a challenging task for the analysts and experts, and entails the need for newer methods and techniques. In this article we present and implement a novel knowledge graph and knowledge mining framework for extracting the relevant information from free-form text about incidents in the cyber domain. The computational framework includes a machine learning-based pipeline for generating graphs of organizations, countries, industries, products and attackers with a non-technical cyber-ontology. The extracted knowledge graph is utilized to estimate the incidence of cyberattacks within a given graph configuration. We use publicly available collections of real cyber-incident reports to test the efficacy of our methods. The knowledge extraction is found to be sufficiently accurate, and the graph-based threat estimation demonstrates a level of correlation with the actual records of attacks. In practical use, an analyst utilizing the presented framework can infer additional information from the current cyber-landscape in terms of the risk to various entities and its propagation between industries and countries.