bluuebunny/crossref_metadata_2025 huggingface dataset:
The diversity of wild Tampoi (Baccaurea, Phyllantaceae) and their potential to improve the livelihoods of local people in Aceh, Indonesia
Authors: Navia Z I , Suwardi A B , Harmawan T
Published: December 2022

Baccaurea are a group of tropical indigenous plants with a high potential of improving food security and public health, particularly in rural areas. The majority of them are found growing wild in the forest and have not been fully explored. Several reports also revealed that the increasing rate of deforestation in recent years, as well as the trend of decreasing knowledge among local people regarding wild species, pose a threat to their existence in nature. As a result, the aim of this study is to determine the diversity of Baccaurea and their relevance to local people in two districts: South Aceh and Southwest Aceh. The plant specimens were collected using an exploratory method, while information on their usage was obtained from literature studies as well as interviews with local people. A total of 9 species were found growing wild in the forests and farmland, such as Baccaurea brevipes Hook.F., B. deflexa Müll.Arg., B. lanceolata Müll.Arg., B. macrocarpa Müll.Arg., B. macrophylla Müll.Arg., B. parviflora Müll.Arg., B. polyneura Hook.F., B. racemosa (Reinw. Ex Bl) Müll.Arg., and B. sumatrana (Miq.) Müll.Arg. All the specimens have the potential to be a source of food, medicinal ingredients, and wood for construction.
Optimization of material formulation and process parameters in canna edulis starch-based biofoam synthesis
Authors: Gabriel A A , Afandi L R P
Published: December 2022

Development of starch based Biofoam rapidly progressed as a solution for minimizing pollution and environmental sustainability. Material formulation and process parameters of Biofoam synthesis were key factors related to the quality of Biofoam products. Canna edulis starch and rice straw powder were used for Biofoam synthesis. The aim of the study was to obtain the optimal formulation of materials and synthesis processes in 5 variations of the formulation with a molding temperature variation of 150 – 170°C using a Manual Thermo-pressing tool. Biofoam synthesized with P3T3 treatment showed the most optimal results with a density 0.4 gr/cm3, tensile strength 2.68 MPa, water absorption capacity 16.41%, and biodegradability 60.08%. The temperature variation treatment has no significant effect on synthesis product due to the adjustment of the printing time to the temperature used. The higher the molding temperature, the shorter the molding duration. The results of the Scanning Electron Microscopy test showed heterogeneous porosity sizes, therefore the mechanical strength was not uniform on the surface of the material. It was known that the average diameter of the Biofoam porosity is in the range of 0.106 – 0.117 mm by using ImageJ.
Analysis of the utilization of rice seeds of improved variety (Inpari 32) in Indramayu District, West Java
Authors: Agustian A , Aldillah R , Nurjati E , Yaumidin U K , Muslim C , Ariningsih E , Rachmawati R R
Published: December 2022

Indramayu is the district with the highest rice production in West Java. Adequate seed availability is required to support its production. This study analyzes the utilization of Inpari 32, an improved rice variety, and its distribution problems. The study was conducted in Indramayu in 2021. The data collected included primary and secondary data. Primary data was gathered by interviewing 30 lowland rice farmers, while secondary data was collected from relevant institutions. Data analysis was done by analyzing farming profitability and varietal distribution. The study’s results show that in Indramayu, the use of Inpari 32 in 2021 reached 45.97% of the total area used for various varieties. Inpari 32 has shifted the dominance of Ciherang variety. The productivity of the Inpari 32 is 7.2 tons/ha GKP, generating a profit of IDR 17.70 million/ha/season. The problem in the distribution of Inpari 32 is the limited availability of seeds and description depicting its superiority. Therefore, Government support for the provision of seeds and socialization of its superiority to increase the dissemination of Inpari 32 is necessary.
Coping strategy of porang farmer’s household in anticipating long harvest period: Empirical study in Wonogiri Regency, Indonesia
Authors: Irianto H , Riptanti E W , Mujiyo
Published: December 2022

Porang is one of the alternative foods commonly cultivated in several areas, including Wonogiri Regency, because this area is suitable for its development. The cultivation business is not devoid of challenges. The tubers of Porang experience a dormancy phase, resulting in a long growing period of 6 to 10 months. Therefore, this study aims to identify the coping strategies used by farmers to adapt the length of the porang harvest period. Furthermore, this study is qualitative in nature involving 180 farmers selected through a census. The snowball sampling method was used to select respondents from 6 sub-districts in Wonogiri Regency in Indonesia. Furthermore, the analysis was conducted descriptively using an index coping strategy for measurement. These results indicated that farmers employ 11 types of coping strategies. The application is performed by combining one type up with more than 4 others. Most of the coping strategies types are applied to 2 combinations, hence, its index is in a low category. The alternative is a realistic combination that farmers can choose based on human and other resource availability.
The characteristics of teapots made of plastic and clay: what are their designs, functions, and impacts on the environment?
Authors: Amboro J L , Purwasito A , Warto
Published: December 2022

Currently, people are starting to reduce the use of traditional products and switch to ready-to-use products made from plastic, such as teapots. Nevertheless, clay crafts still maintain their existence in the widespread use of plastic products. Bayat is one of the subdistricts in Klaten Regency, Central Java, which is famous for its ceramics and pottery craft centres. Most artisans in the Bayat make crafts with clay as raw materials. This research focused on the advantages of Bayat pottery over other plastic products. This study aimed to increase public awareness to reduce plastic products’ use in daily life. This study used the descriptive qualitative method. The research was conducted in Bayat, Klaten, from March – June 2022. The results showed that clay crafts were considered more eco-friendly than plastic products. The development of Bayat pottery from clay has implications for design, function, usability, and environmental aspects. In the design aspect, the Bayat teapot can increase the aesthetic value of the craft. In terms of function and usability, the clay teapot functions as a water storage container as well as interior decoration. Meanwhile, in the environmental aspect, raw clay materials are easier to decompose, while plastic products are difficult to decompose.
Information Costs and the Civil Justice System
Authors: Hylton Keith N
Published: December 2022

Litigation is costly because information is not free. Given that information is costly and perfect information prohibitively costly, courts will occasionally err. Finally, the fact that information is costly implies an unavoidable degree of informational asymmetry between disputants. This paper presents a model of the civil justice system that incorporates these features and probes its implications for compliance with the law, efficiency of law, accuracy in adjudication, trial outcome statistics, and the evolution of legal standards. The model’s claims are applied to and tested against the relevant empirical and legal literature.
Cardiac metabolism in HFpEF: from fuel to signalling
Authors: Capone Federico , Sotomayor-Flores Cristian , Bode David , Wang Rongling , Rodolico Daniele , Strocchi Stefano , Schiattarella Gabriele G
Published: December 2022

Heart failure (HF) is marked by distinctive changes in myocardial uptake and utilization of energy substrates. Among the different types of HF, HF with preserved ejection fraction (HFpEF) is a highly prevalent, complex, and heterogeneous condition for which metabolic derangements seem to dictate disease progression. Changes in intermediate metabolism in cardiometabolic HFpEF—among the most prevalent forms of HFpEF—have a large impact both on energy provision and on a number of signalling pathways in the heart. This dual, metabolic vs. signalling, role is played in particular by long-chain fatty acids (LCFAs) and short-chain carbon sources [namely, short-chain fatty acids (SCFAs) and ketone bodies (KBs)]. LCFAs are key fuels for the heart, but their excess can be harmful, as in the case of toxic accumulation of lipid by-products (i.e. lipotoxicity). SCFAs and KBs have been proposed as a potential major, alternative source of energy in HFpEF. At the same time, both LCFAs and short-chain carbon sources are substrate for protein post-translational modifications and other forms of direct and indirect signalling of pivotal importance in HFpEF pathogenesis. An in-depth molecular understanding of the biological functions of energy substrates and their signalling role will be instrumental in the development of novel therapeutic approaches to HFpEF. Here, we summarize the current evidence on changes in energy metabolism in HFpEF, discuss the signalling role of intermediate metabolites through, at least in part, their fate as substrates for post-translational modifications, and highlight clinical and translational challenges around metabolic therapy in HFpEF.
Cropbox: a declarative crop modelling framework
Authors: Yun Kyungdahm , Kim Soo-Hyung
Published: December 2022

We introduce Cropbox, a novel modelling framework that supports various aspects of crop modelling in a unique yet concise style. Building a crop model can be easily riddled with technical details looking trivial at first but later becoming major obstacles that hamper the whole development or application process. This is particularly the case when implementing models from scratch without relying on an established framework. Cropbox adopts a declarative approach providing a domain-specific language to reduce technical debt and assist modellers to focus on high-level abstraction formed by relations between variables and enclosing systems, rather than tinkering with low-level implementation details. The syntax of Cropbox framework is based on the Julia programming language and is deliberately constrained to avoid unintended side effects caused by common mistakes while its architecture remains open to extension. We highlight key capabilities of the framework through case studies featuring a leaf gas-exchange model and a whole-plant simulation model. We also illustrate potential extensions for supporting functional-structural plant modelling by demonstrating a 3D root architectural model as an example.
Perceived Fairness Concerns Within Pandemic Response Technology
Authors: Ryan Seamus , Nurgalieva Leysan , Doherty Gavin
Published: December 2022

The response to the spread of the COVID-19 pandemic has involved the creation of complex, novel public health technologies deployed at an unprecedented scale. One such technology intervention is the deployment of digital COVID certificates, applications that confirm a person’s COVID-19 immunity status via vaccination, negative tests or having contracted the disease. These certificates have formed part of governmental strategies to manage the resumption of travel and social activities. The potential impact of these technologies on daily life has led to perceived concerns regarding the fairness of the restrictions associated with these systems. These fairness concerns are intuitively understood by users, and challenges exist in conceptualizing them in a manner that is addressable with the tools available to application and system designers. In order to improve our understanding of the fairness concerns of users and how we might conceptualize them, we analysed 27 semi-structured interviews with Irish participants regarding the use of digital immunity certificates. Our results suggest that the user perceptions of the fairness of such solutions are primarily thought about at the group level, with the concerns of Anti-discrimination and Egalitarianism being the most frequently discussed. Based on our analysis, we further identify societal and technical accessibility as important factors when attempting to address these fairness concerns.
Sensitive immunoassay ofLegionellausing multivalent conjugates of engineered VHHs
Authors: Kiyose Norihiko , Miyazaki Nobuo , Furuhata Katsunori , Ito Yuji
Published: December 2022

VHH antibodies or nanobodies, which are antigen-binding domains of heavy chain antibodies from camelid species, have several advantageous characteristics, including compact molecular size, high productibility in bacteria and easy engineering for functional improvement. Focusing on these advantages of VHHs, we attempted to establish an immunoassay system for detection of Legionella, the causative pathogen of Legionnaires’ disease. A VHH phage display library was constructed using cDNA from B cells of alpacas immunized with Legionella pneumophila serogroup1 (LpSG1). Through biopanning, two specific VHH clones were isolated and used to construct a Legionella detection system based on the latex agglutination assay. After engineering the VHHs and improving the assay system, the sensitive detection system was successfully established for the LpSG1 antigen. The immunoassay developed in this study should be useful in easy and sensitive detection of Legionella, the causative agent of Legionnaires’ disease, which is a potentially fatal pneumonia.
Mathematical formulation and an improved moth–flame optimization algorithm for parallel two-sided disassembly line balancing based on fixed common stations
Authors: Zhang Yu , Zhang Zeqiang , Yin Tao , Liang Wei
Published: December 2022

Nowadays, rapid product iterations result in large quantities of end-of-life products. To meet the fast-growing demand for remanufacturing engineering, companies have quickened the standardization and industrialization of waste dissembling. Two-sided disassembly lines can effectively disassemble large-sized products on both sides of the lines, and parallel disassembly lines can disassemble multiple products simultaneously with fewer workstations and higher production efficiency. Combining the two types of disassembly can effectively increase the disassembly efficiency of large-sized products. However, the parallel two-sided disassembly line has not been fully investigated because of the essential complexity of the problem. Therefore, this research introduced the parallel two-sided disassembly line balancing problem with fixed common stations. First, a multi-objective mixed-integer programming model is established to solve the problem for the first time. The model is proved to be correct through small-scale numerical examples. Second, a multi-objective improved moth–flame optimization algorithm is implemented to solve the proposed large-scale problems. The proposed algorithm employs a two-phase decoding approach to design the scheme and a discrete moth for fire operation to search and replace new individuals, and then a restart strategy is introduced to reduce the probability of the population falling into a local optimum. Finally, the algorithm solved extensive disassembly line balancing problems with different layouts, including the straight-line, two-sided, and parallel two-sided, and case studies demonstrated the reliability and validity of the proposed method.
Translation, cross-cultural adaptation and validation of the Health Belief Model Questionnaire (HBMQ) for weight management behaviour for use in a Southeast Asian country
Authors: Raman Sivasankari , Ong Siew Chin , Ooi Guat See
Published: December 2022

Objectives

In the past 50 years, obesity and being overweight have become significant health concerns that cause a rise in the risk of illness, impairing quality of life and increasing financial burdens worldwide. The purpose of the study is to conduct translation and cross-cultural adaptation of a Health Belief Model Questionnaire (HBMQ) for weight management behaviour into the Malay language and to validate the questionnaire.

Methods

The HBMQ was adapted and translated into the Malay language based on published international guidelines. The content validity and the face validity were analysed by a panel of 10 experts. A pilot test was conducted with 35 students from Universiti Sains Malaysia to evaluate internal consistency. A cross-sectional study was carried out by distributing the self-administered HBMQ to the general public in Malaysia and 505 subjects were successfully recruited. The construct validity was evaluated by exploratory factor analysis. The first 112 participants completed the survey again one week later for the evaluation of test-retest reliability.

Key findings

In total, 79 questions had an item-level content validity index (I-CVI) score of >0.80 and have been evaluated as excellent inferring acceptable content validity. The remaining seven items in the instrument had an I-CVI score < 0.80 and were removed based on the experts’ consensus. The item-level face validity index value for each item range was between 0.8 and 1.0, indicating a satisfactory level of face validity. For construct validity, eight factors were requested and 74 items had a significant to strong factor loading of >0.4. The rotation of items showed five items had factor loadings <0.4 (item numbers 14, 57, 77, 78 and 79) and have been removed.

Conclusions

The findings in this study conclude that the translated Health Belief Model-Malay version has adequate content validity, face validity, construct validity and reliability.
Comparison of the clinical outcomes following total knee arthroplasty in osseous ankylosed and non-ankylosed knees using propensity-score matching
Authors: Kii Sakumo , Sonohata Motoki , Nakashima Takema , Hashimoto Akira , Ueno Masaya , Mawatari Masaaki
Published: December 2022

Objectives

Few studies have compared the clinical outcomes and complications of total knee arthroplasty (TKA) in patients with and without osseous ankylosed knees. Thus, we investigated the clinical outcomes and complications of TKA in patients with osseous ankylosed knees using a propensity-score matching method.

Methods

Thirteen knees in the osseous ankylosed-knees group and 13 knees in the non-ankylosed-knees group were included after excluding those with less than 2 years of follow-up or a lack of data and after propensity-score matching. The American Knee Society Score-knee (AKSS-knee), AKSS-function, knee-flexion angle, knee-extension angle, knee range of motion (ROM) before and after TKA, and the number of knees with postoperative complications were evaluated as primary outcomes.

Results

The AKSS-knee, AKSS-function, knee-flexion angle, and knee ROM in the osseous ankylosed-knees group after TKA were significantly lower than those in the non-ankylosed-knees group. The knee-extension angle after TKA and number of knees with postoperative complications within 2 years were not significantly different between the two groups.

Conclusions

The clinical results of TKA in patients with osseous ankylosed knees were inferior to those in patients with non-ankylosed knees.
Antibiotic Susceptibility Profile for the US Neisseria meningitidis Urethritis Clade
Authors: Bazan Jose A , Tzeng Yih-Ling , Bischof Katarina M , Satola Sarah W , Stephens David S , Edwards Jennifer L , Carter Alexandria , Snyder Brandon , Turner Abigail Norris
Published: December 2022

The US Neisseria meningitidis urethritis clade (US_NmUC) harbors gonococcal deoxyribonucleic acid alleles and causes gonorrhea-like urogenital tract disease. A large convenience sample of US_NmUC isolates (N = 122) collected between January 2015 and December 2019 in Columbus, Ohio demonstrated uniform susceptibility to antibiotics recommended for gonorrhea treatment and meningococcal chemoprophylaxis.
A Turtle Disaster: Salmonella enteritidis Cardiovascular Implantable Electronic Device Infection
Authors: Brenneman Ethan , Keil Elizabeth , Advani Sonali D , Campbell Kristen Bova , Wrenn Rebekah
Published: December 2022

Cardiovascular implantable electronic device (CIED) infections have high mortality and morbidity. CIED infections secondary to gram-negative pathogens are rare, and there are few data regarding their treatment. We report a case of a 60-year-old male who developed recurrent Salmonella enteritidis bacteremia leading to CIED infection and nonsusceptibility to ciprofloxacin.
The Impact of a Walk-in Human Immunodeficiency Virus Care Model for People Who Are Incompletely Engaged in Care: The Moderate Needs (MOD) Clinic
Authors: Kumbhakar Raaka G , Budak Jehan Z , Tao Yuan , Beste Jason , Lake Eve , Navabi Nazlee , Mose Eric , Barker Gwen , Lee Ji , Hara Katie , Khosropour Christine , Dhanireddy Shireesha , Dombrowski Julia C
Published: December 2022

Background

The Moderate Needs (MOD) Clinic in Seattle, Washington provides walk-in primary care for people with human immunodeficiency virus (HIV) who are incompletely engaged in standard care.

Methods

We evaluated HIV outcomes among patients enrolled in the MOD Clinic (within group analysis) and, separately, among MOD patients versus patients who were MOD-eligible but did not enroll (comparison group analysis) during January 1, 2018–September 30, 2021. The primary outcome was viral suppression ([VS] viral load <200 copies/mL); secondary outcomes care engagement (≥2 visits ≥60 days apart) and sustained VS (≥2 consecutive suppressed viral loads ≥60 days apart). In the within group analysis, we examined outcomes at time of MOD enrollment versus 12 months postenrollment. In the comparison group analysis, we examined outcomes at the time of MOD eligibility versus 12 months posteligibility. Both analyses used modified Poisson regression.

Results

Most patients in MOD (N = 213) were unstably housed (52%) and had psychiatric comorbidities (86%) or hazardous substance use (81%). Among patients enrolled ≥12 months (N = 164), VS did not increase significantly from baseline to postenrollment (63% to 71%, P = .11), but care engagement and sustained VS both improved (37% to 86%, P < .001 and 20% to 53%, P < .001, respectively) from pre-enrollment to 12 months postenrollment. In the comparison group analysis, VS worsened in nonenrolled patients (N = 517) from baseline to 12 months posteligibility (82% to 75%, P < .001). Patients in the MOD Clinic who met criteria for the comparison group analysis (N = 68) were more likely than nonenrolled patients to be engaged in care at 12 months posteligibility (relative risk, 1.29; 95% confidence interval, 1.03–1.63).

Conclusions

The MOD Clinic enrollment was associated with improved engagement in care. This model adds to the spectrum of differentiated HIV care services.
Identifying Patient-Centered Outcomes for Caregivers and Children With Musculoskeletal Infections
Authors: Wood James B , Hawryluk Bridget , Lynch Dustin , Claxton Gina , Russell Kelsey , Bennett William E , Wiehe Sarah E , Carroll Aaron E
Published: December 2022

Background

Musculoskeletal infections (MSKI), including osteomyelitis and septic arthritis, are among the most common invasive infections in children and have the potential to cause significant morbidity. Guidelines have been developed to optimize care based on clinician-developed endpoints. Patient-centered outcomes have not been defined for children with MSKI. This study identified outcomes most important to caregivers and patients with MSKI.

Methods

This was a single-center prospective qualitative study of children 6 months to 18 years of age hospitalized with MSKI from November 2019 to September 2021. Using design-research methods, patients and caregivers participated in interviews and/or completed journals to describe their experiences during acute infection and recovery from MSKI.

Results

A total of 51 patient/caregivers were approached to participate in the study, 35 of whom declined to participate, resulting in 8 interviews conducted and 14 journals collected from 16 patient/caregivers. From these, a journey map was created highlighting points of stress during the onset of symptoms, through hospitalization, and returning home with new challenges. In addition, patient-centered outcomes were identified. For caregivers, these included managing mental health, managing responsibilities, and receiving support. Both caregivers and patients shared the importance of understanding of treatment plans and responsibilities. For patients, improving mental and physical health was important.

Conclusions

Management of children with MSKI is complex and requires a multidisciplinary team approach. Validation of the outcomes identified and development of a measurement tool are needed. Addressing the patient-centered outcomes we identified in this study can greatly improve the holistic care of children with MSKI.
Modeling of geocoronal solar wind charge exchange events detected with Suzaku
Authors: Ishi Daiki , Ishikawa Kumi , Miyoshi Yoshizumi , Terada Naoki , Ezoe Yuichiro
Published: December 2022

A model of geocoronal solar wind charge exchange (SWCX) emission was built and compared to five Suzaku detections of bright geocoronal SWCX events. An exospheric neutral hydrogen distribution model, charge exchange cross-sections, solar wind ion data taken with the ACE and WIND satellites, and magnetic field models of the Earth’s magnetosphere are all combined in order to predict time-variable geocoronal SWCX emission depending on line-of-sight directions of the Suzaku satellite. The modeled average intensities of O vii emission lines were consistent with the observed ones within a factor of three in four out of the five cases except for an event in which a line-of-sight direction was toward the night side of the high-latitude magnetosheath and a major geomagnetic storm was observed. Those of O viii emission lines were underestimated by a factor of three or more in all five cases. On the other hand, the modeled O vii and O viii light curves reproduced the observed ones after being scaled by ratios between the observed and modeled average intensities. In particular, short-term variations due to line-of-sight directions traversing cusp regions during an orbital motion of the Suzaku satellite were reproduced. These results are discussed in the context of model uncertainties.
A biophysical model of viral escape from polyclonal antibodies
Authors: Yu Timothy C , Thornton Zorian T , Hannon William W , DeWitt William S , Radford Caelan E , Matsen Frederick A , Bloom Jesse D
Published: December 2022

A challenge in studying viral immune escape is determining how mutations combine to escape polyclonal antibodies, which can potentially target multiple distinct viral epitopes. Here we introduce a biophysical model of this process that partitions the total polyclonal antibody activity by epitope and then quantifies how each viral mutation affects the antibody activity against each epitope. We develop software that can use deep mutational scanning data to infer these properties for polyclonal antibody mixtures. We validate this software using a computationally simulated deep mutational scanning experiment and demonstrate that it enables the prediction of escape by arbitrary combinations of mutations. The software described in this paper is available at https://jbloomlab.github.io/polyclonal.
Effects of hydroxychloroquine on atrial electrophysiology in in silico wild-type and PITX2+/- atrial cardiomyocytes
Authors: Song Euijun
Published: December 2022

Hydroxychloroquine (HCQ) is commonly used in the treatment of autoimmune diseases and increases the risk of QT interval prolongation. We quantitatively examined the potential atrial arrhythmogenic effects of HCQ on atrial fibrillation (AF) using a computational model of human atrial cardiomyocytes. We measured atrial electrophysiological markers after systematically varying HCQ concentrations. HCQ concentrations were positively correlated with the action potential duration (APD), resting membrane potential, refractory period, APD alternans threshold, and calcium transient alternans threshold (P<0.05). In contrast, HCQ concentrations were inversely correlated with the maximum upstroke velocity and calcium transient amplitude (P<0.05). When the therapeutic concentration (Cmax) of HCQ was applied, HCQ increased APD90 by 1.4% in normal sinus rhythm, 1.8% in wild-type AF, and 2.6% in PITX2+/- AF, but did not affect the alternans thresholds. The overall in silico results suggest no significant atrial arrhythmogenic effects of HCQ at Cmax, rather implying a potential antiarrhythmic role of low-dose HCQ in AF. However, at HCQ of 4-fold Cmax, a rapid pacing rate of 4 Hz could induce prominent APD alternans, particularly in the PITX2+/- AF model. Concomitant PITX2 mutations and HCQ treatments may increase the risk of AF, and this potential arrhythmogenic effect of HCQ should be further investigated.
Plasmodesmal connectivity in C4Gynandropsis gynandrais induced by light and dependent on photosynthesis
Authors: Schreier Tina B. , Müller Karin H. , Eicke Simona , Faulkner Christine , Zeeman Samuel C. , Hibberd Julian M.
Published: December 2022

In leaves of C4plants the reactions of photosynthesis become restricted between two compartments. Typically, this allows accumulation of C4acids in mesophyll cells and subsequent decarboxylation in the bundle sheath. In C4grasses proliferation of plasmodesmata between these cell types is thought to increase cell-to-cell connectivity to allow efficient metabolite movement. However, it is not known if C4dicotyledons also show this enhanced plasmodesmal connectivity and so whether this is a general requirement for C4photosynthesis is not clear. How mesophyll and bundle sheath cells in C4leaves become highly connected is also not known.

We investigated these questions using 3D- and 2D- electron microscopy on the C4dicotyledonGynandropsis gynandraas well as phylogenetically close C3relatives.

The mesophyll-bundle sheath interface of C4G. gynandrashowed higher plasmodesmal frequency compared with closely related C3species. Formation of these plasmodesmata was induced by light. Pharmacological agents that perturbed chloroplast development or photosynthesis reduced the number of plasmodesmata, but this inhibitory effect could be reversed by the provision of exogenous sucrose.

We conclude that enhanced formation of plasmodesmata between mesophyll and bundle sheath cells is wired to the induction of photosynthesis in C4G. gynandra.
Spatial-temporal order-disorder transition in angiogenic NOTCH signaling controls cell fate specification
Authors: Kang Tae-Yun , Bocci Federico , Nie Qing , Onuchic José Nelson , Levchenko Andre
Published: December 2022

Angiogenesis is a morphogenic process resulting in the formation of new blood vessels from pre-existing ones, usually in hypoxic micro-environments. The initial steps of angiogenesis depend on robust differentiation of oligopotent endothelial cells into the Tip and Stalk phenotypic cell fates, controlled by NOTCH-dependent cell-cell communication. The dynamics of spatial patterning of this cell fate specification are only partially understood. Here, by combining a controlled experimental angiogenesis model with mathematical and computational analyses, we find that the regular spatial Tip-Stalk cell patterning can undergo an order-disorder transition at a relatively high input level of a pro-angiogenic factor VEGF. The resulting differentiation is robust but temporally unstable for most cells, with only a subset of presumptive Tip cells leading sprout extensions. We further find that sprouts form in a manner maximizing their mutual distance, consistent with a Turing-like model that may depend on local enrichment and depletion of fibronectin. Together, our data suggest that NOTCH signaling mediates a robust way of cell differentiation enabling but not instructing subsequent steps in angiogenic morphogenesis, which may require additional cues and self-organization mechanisms. This analysis can assist in further understanding of cell plasticity underlying angiogenesis and other complex morphogenic processes.

Significance Statement

We investigate the spatial and temporal patterns of Tip/Stalk specification and the ensuing angiogenic sprouting by using a novel controlled micro-engineered experimental model of angiogenesis and a set of mathematical models of the spatially resolved, cell population-level VEGF-NOTCH signaling. Our analysis provides a dynamic view of the initial step of angiogenesis, revealing fluctuations in its onset, and features suggesting transitions between order and disorder in cell organization. These findings suggest how a potentially very restrictive patterning mechanism can become sensitive to a variety of environmental cues. This sensitivity can be crucial for proper vascularization of a damaged organ, and may suggest new ways of analyzing angiogenesis in the context of cancer and other pathologies. This analysis also suggests a framework for understanding of other instances of NOTCH-mediated patterning processes.
Cis-Regulatory Atlas in Primary Human CD4+ T Cells
Authors: Stefan Kurtis , Barski Artem
Published: December 2022

Cis-regulatory elements (CRE) are critical for coordinating gene expression programs that dictate cell-specific differentiation and homeostasis. Recently developed self-transcribing active regulatory region sequencing (STARR-Seq) has allowed for genome-wide annotation of functional CREs. Despite this, STARR-Seq assays are only employed in cell lines, in part, due to difficulties in delivering reporter constructs. Herein, we implemented and validated a STARR-Seq–based screen in human CD4+ T cells using a non-integrating lentiviral transduction system. Lenti-STARR-Seq is the first example of a genome-wide assay of CRE function in human primary cells, identifying thousands of functional enhancers and negative regulatory elements (NREs) in human CD4+ T cells. Results of the screen were validated using traditional luciferase assays. Genome-wide, we find clear differences between enhancers and NREs in nucleosome positioning, chromatin modification, eRNA production, and transcription factor binding. Our findings support the idea of silencer repurposing as enhancers in alternate cell types. Collectively, these data suggest that Lenti-STARR-Seq is a can be used for CRE screening in primary human cell types.
Convergent adaptation of true crabs (Decapoda: Brachyura) to a gradient of terrestrial environments
Authors: Wolfe Joanna M. , Ballou Lauren , Luque Javier , Watson-Zink Victoria M. , Ahyong Shane T. , Barido-Sottani Joëlle , Chan Tin-Yam , Chu Ka Hou , Crandall Keith A. , Daniels Savel R. , Felder Darryl L. , Mancke Harrison , Martin Joel W. , Ng Peter K.L. , Ortega-Hernández Javier , Theil Emma Palacios , Pentcheff N. Dean , Robles Rafael , Thoma Brent P. , Tsang Ling Ming , Wetzer Regina , Windsor Amanda M. , Bracken-Grissom Heather D.
Published: December 2022

For much of terrestrial biodiversity, the evolutionary pathways of adaptation from marine ancestors are poorly understood, and have usually been viewed as a binary trait. True crabs, the decapod crustacean infraorder Brachyura, comprise over 7,600 species representing a striking diversity of morphology and ecology, including repeated adaptation to non-marine habitats. Here, we reconstruct the evolutionary history of Brachyura using new and published sequences of 10 genes for 344 tips spanning 88 of 109 brachyuran families. Using 36 newly vetted fossil calibrations, we infer that brachyurans most likely diverged in the Triassic, with family-level splits in the late Cretaceous and early Paleogene. By contrast, the root age is underestimated with automated sampling of 328 fossil occurrences explicitly incorporated into the tree prior, suggesting such models are a poor fit under heterogeneous fossil preservation. We apply recently defined trait-by-environment associations to classify a gradient of transitions from marine to terrestrial lifestyles. We estimate that crabs left the marine environment at least seven and up to 17 times convergently, and returned to the sea from non-marine environments at least twice. Although the most highly terrestrial- and many freshwater-adapted crabs are concentrated in Thoracotremata, Bayesian threshold models of ancestral state reconstruction fail to identify shifts to higher terrestrial grades due to the degree of underlying change required. Lineages throughout our tree inhabit intertidal and marginal marine environments, corroborating the inference that the early stages of terrestrial adaptation have a lower threshold to evolve. Our framework and extensive new fossil and natural history datasets will enable future comparisons of non-marine adaptation at the morphological and molecular level. Crabs provide an important window into the early processes of adaptation to novel environments, and different degrees of evolutionary constraint that might help predict these pathways.
Quinazoline-quinoline bisubstrate inhibitors target eukaryotic translation initiation factor 3 inPlasmodium falciparum
Authors: Dobrescu Irina , Hammam Elie , Dziekan Jerzy M. , Claës Aurélie , Halby Ludovic , Preiser Peter , Bozdech Zbynek , Arimondo Paola B. , Scherf Artur , Nardella Flore
Published: December 2022

Malaria drug resistance is hampering the fight against the deadliest parasitic disease affecting over 200 million people worldwide. We recently developed quinoline-quinazoline-based inhibitors (as compound70) as promising new antimalarials. Here we aimed to investigate their mechanism of action by using Thermal Proteome Profiling (TPP). The eukaryotic translation initiation factor 3 (EIF3i) subunit I was identified as the main target of the inhibitor inP. falciparum. This protein is not a known drug target in malaria parasites.P. falciparumparasite lines were generated expressing either a HA tag or an inducible knockdown of the PfEIF3i gene to further characterize the target protein. PfEIF3i was stabilized in presence of the compound70in a cellular thermal shift-western blot assay, confirming that PfEIF3i is a target of quinoline-quinazoline-based inhibitors. In addition, PfEIF3i-inducible knock-down blocks intra-erythrocytic development in the trophozoite stage indicating that it has a vital function. We show that PfEIF3i is mostly expressed in late intraerythrocytic stages and localizes in the cytoplasm. Previous mass spectrometry reports show that EIF3i is expressed in all parasite life cycle stages. Hence, quinoline-quinazoline-based inhibitors allowed to identify PfEIF3i as a valuable target for the design of new antimalarial drugs active all along the life cycle of the parasite.
Focused ultrasound-mediated brain genome editing
Authors: Lao Yeh-Hsing , Ji Robin , Zhou Joyce K. , Snow Kathy J. , Kwon Nancy , Saville Ethan , He Siyu , Chauhan Shradha , Chi Chun-Wei , Datta Malika S. , Zhang Hairong , Quek Chai Hoon , Cai Sarah , Li Mingqiang , Gaitan Yaned , Bechtel Lawrence , Wu Shih-Ying , Lutz Cathleen M. , Tomer Raju , Murray Stephen A. , Chavez Alejandro , Konofagou Elisa E. , Leong Kam W.
Published: December 2022

Gene editing in the mammalian brain has been challenging because of the restricted transport imposed by the blood-brain barrier (BBB). Current approaches rely on local injection to bypass the BBB. However, such administration is highly invasive and not amenable to treating certain delicate regions of the brain. We demonstrate a safe and effective gene editing technique by using focused ultrasound (FUS) to transiently open the BBB for the transport of intravenously delivered CRISPR/Cas9 machinery to the brain.
The SUMO-interacting Motif in NS2 promotes adaptation of avian influenza virus to mammals
Authors: Sun Liuke , Kong Huihui , Yu Mengmeng , Zhang Zhenyu , Zhang Haili , Na Lei , Qu Yuxing , Zhang Yuan , Chen Hualan , Wang Xiaojun
Published: December 2022

Species differences in the host factor ANP32A/B result in the restriction of avian influenza virus polymerase (vPol) in mammalian cells. Efficient replication of avian influenza viruses in mammalian cells often requires adaptive mutations, such as PB2-E627K, to enable the virus to utilize mammalian ANP32A/B. However, the molecular basis for the productive replication of avian influenza viruses without prior adaptation in mammals remain poorly understood. We show that influenza A virus protein NS2 help to overcome mammalian ANP32A/B-mediated restriction to avian vPol activity by promoting avian vRNP assembly and enhancing mammalian ANP32A/B-vRNP interactions. A conserved SUMO interaction motif (SIM) in NS2 is required for its avian polymerase-enhancing properties. We also demonstrate that disrupting SIM integrity in NS2 impairs avian influenza virus replication and pathogenicity in mammalian hosts, but not in avian hosts. Our results identify NS2 as a cofactor in the adaptation process of avian influenza viruses to mammals.
A retrospective study of knowledge management for integrated resorts (IRs) crisis preparedness
Authors: Zhang Su , Hsu Fu-Chieh , Zhang Yang
Published: December 2022

Purpose

This study aims to propose a systematic knowledge management model to explore the causal links leading to the organizational crisis preparedness (OCP) level of integrated resorts (IRs) during the COVID-19 pandemic based on the intangible capital of organizational climate, dynamic capability, substantive capability and commitment.

Design/methodology/approach

The authors use data obtained from IRs in Macau. The Wuli–Shili–Renli (WSR) approach underpins the study. Structural equation modeling following fuzzy-set qualitative comparative analysis (fsQCA) was used for data processing.

Findings

The results showed that organizational climate has an essential role in IRs preparedness for crises and affects their dynamic capacity, substantive capacity and commitment. The fsQCA results revealed that the relationships between conditions with a higher level of dynamic and substantive capability lead to higher OCP scores.

Practical implications

Executives should develop systemic thinking regarding organization preparedness in IRs for crisis management. A comprehensive understanding of the IRs’ business environment and crises is necessary, as they will require different factor constellations to allow the organization to perform well in a crisis. Financial support for employees could ensure their assistance when dealing with such situations. Rapid response teams should be set up for daily operations and marketing implementation of each level of the IRs management systems.

Originality/value

This study contributes to the extant literature on IRs crisis management in the OCP aspect. The authors constructed a systematic composite picture of organization executives’ knowledge management through the three layers of intangible capitals in WSR. Moreover, the authors explored causal links of WSR from symmetric and asymmetric perspectives.
Invasive plants have greater growth than co‐occurring natives in live soil subjected to a drought‐rewetting treatment
Authors: Zhang Xue , Oduor Ayub M. O. , Liu Yanjie
Published: December 2022

Several studies have shown that invasive plant species respond more negatively to drought than native plant species, but little remains understood of how and whether drought‐rewetting events may affect growth of invasive and co‐occurring native plant species both directly and indirectly through soil microorganisms.

In a fully crossed factorial design, we grew individuals of four congeneric pairs of invasive and native plant species in 2.5 L pots that contained live or sterilized field soil under one of three drought treatments: no‐drought, drought, drought‐rewetting.

Results show that drought caused a significantly greater decline in total biomass of invasive plant species than that of native plant species regardless of the presence of live soil microorganisms. However, total biomass of the invasive plant species exhibited a greater recovery from drought following rewetting than did that of the native plant species. Moreover, recovery from drought in invasive plant species tended to be stronger in live soil than in sterilized soil, while for the native plant species, recovery from drought was stronger in sterilized soil than in live soil.

Overall, these results suggest that in ecosystems that experience cycles of drought and rewetting, invasive plant species may grow larger than co‐occurring native plant species. Moreover, soil microorganisms may facilitate greater recovery from drought in invasive plant species than in co‐occurring native plant species.

Read the free Plain Language Summary for this article on the Journal blog.
Sex‐specific differences in T‐cell immune dysregulation and aberrant response to inflammatory stimuli in offspring exposed to maternal chronic inflammation
Authors: Liu Jin , Liu Yang , Kirschen Gregory , Liu Anguo , Lei Jun , Burd Irina
Published: December 2022

Problems

Maternal chronic inflammation (MI) can adversely affect offspring's immune development resulting in dysregulation of splenic T cells. Interleukin 1 beta (IL‐1β) contributes to mediating inflammation in the placenta to induce fetal toxicity and cause long‐term postnatal sequelae. In this study, we investigated how MI affects the T‐cell immune development from the fetal to the neonatal period and how offspring responded to postnatal IL‐1β challenge when exposed to an adverse intrauterine environment. We also extend these studies to examine the sex‐specific differences.

Methods of Study

Time‐pregnant CD1 dams were administrated with four consecutive injections of mouse recombinant Interleukin‐1β (rIL‐1β) or phosphate‐buffered saline (PBS) from embryonic day (E)14 to E17. Pups were treated with rIL‐1β or PBS at postnatal day (PND)11 (pre‐weaning) or PND24 (post‐weaning). Pups’ splenic immune cells were isolated and then characterized using flow cytometry.

Results

At PND12, no differences were observed either in Ctrl or MI offspring. At PND25, we observed elevated amount of CD8+ T cells, descending CD4+/CD8+ and Treg/Teff ratio in MI offspring. Pre‐weaning rIL‐1β administration did not affect T‐cell subpopulation in Ctrl pups while post‐weaning rIL‐1β administration increased T cells and CD8+ T cells and decreased CD4+/CD8+ and Treg/Teff ratio in Ctrl offspring. Furthermore, pre‐weaning rIL‐1β administration decreased the frequency of T cells and Treg/Teff ratio in MI pups while post‐weaning rIL‐1β administration increased Tregs and Treg/Teff in MI pups. Regarding sex‐specific changes, we observed that at PND12, MI females exhibited higher CD4+/CD8+ and Treg/Teff ratio than Ctrl females. At PND25, we observed elevated amount of CD8+ T cells, descending CD4+/CD8+ and Treg/Teff ratio in MI Females, while MI males did not show any changes in T‐cell population. Pre‐weaning rIL‐1β administration decreased T‐cell frequency in both MI males and females and decreased Treg/Teff ratio only in MI females. Post‐weaning rIL‐1β administration increased Tregs and Treg/Teff ratio, and decreased CD4+/CD8+ ratio in MI females.

Conclusions

Prenatal‐inflammation‐exposed offspring exhibited dysfunctional T‐cell immunity and regulatory immune responses to postnatal challenges, showing both sex‐specific and age‐dependent differences. It could be speculated from our results that experiencing environmental challenges or adverse stimuli during the vulnerable intrauterine period, such as maternal chronic inflammation, stress, preterm birth, and chronic infections, might induce fetal immune reprogramming and potentially cause long‐term adverse immune consequences, such as a predisposition to allergic diseases, autoimmune diseases, asthma and pediatric mortality of unknown etiology.