bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Climatic Variability Hypothesis and trade-offs in thermal performance in coastal and inland populations ofMimulus guttatus
Authors: Chiono Alec , Paul John R 
Published: January 2023

AbstractEcologists and evolutionary biologists have long predicted that organisms in more climatically variable environments should be adapted to handle a wider range of conditions. This intuitive idea, known as the Climatic Variability Hypothesis (CVH), has gained mixed support from empirical studies. We tested the CVH in a novel system by comparing the thermal breadth of coastal and inland populations of Mimulus guttatus. To quantify thermal breadth, we performed a thermal performance experiment and built performance curves. Using these performance curves, we also evaluated evidence for a breadth-performance trade-off and the Hotter-is-Better hypothesis. We did not find support for the CVH; coastal and inland populations did not differ in thermal breadth. However, we found evidence for a breadth-performance trade-off and the Hotter-is-Better hypothesis. Surprisingly, the two most inland populations differed the most in the thermal performance traits we evaluated. Our results highlight the importance of explicitly measuring thermal performance to test explanations of species distribution patterns and the need to examine alternative mechanisms by which organisms occupy different climatic regimes.
Microbial ecology of vertebrate decomposition in terrestrial ecosystems
Authors: Mason Allison R , Taylor Lois S , DeBruyn Jennifer M 
Published: January 2023

AbstractVertebrate decomposition results in an ephemeral disturbance of the surrounding environment. Microbial decomposers are recognized as key players in the breakdown of complex organic compounds, controlling carbon and nutrient fate in the ecosystem and potentially serving as indicators of time since death for forensic applications. As a result, there has been increasing attention on documenting the microbial communities associated with vertebrate decomposition, or the ‘necrobiome’. These necrobiome studies differ in the vertebrate species, microhabitats (e.g. skin vs. soil), and geographic locations studied, but many are narrowly focused on the forensic application of microbial data, missing the larger opportunity to understand the ecology of these communities. To further our understanding of microbial dynamics during vertebrate decomposition and identify knowledge gaps, there is a need to assess the current works from an ecological systems perspective. In this review, we examine recent work pertaining to microbial community dynamics and succession during vertebrate (human and other mammals) decomposition in terrestrial ecosystems, through the lens of a microbial succession ecological framework. From this perspective, we describe three major microbial microhabitats (internal, external, and soil) in terms of their unique successional trajectories and identify three major knowledge gaps that remain to be addressed.
The first gapless, reference-quality, fully annotated genome from a Southern Han Chinese individual
Authors: Chao Kuan-Hao , Zimin Aleksey V , Pertea Mihaela , Salzberg Steven L 
Published: January 2023

Abstract
We used long-read DNA sequencing to assemble the genome of a Southern Han Chinese male. We organized the sequence into chromosomes and filled in gaps using the recently completed T2T-CHM13 genome as a guide, yielding a gap-free genome, Han1, containing 3,099,707,698 bases. Using the T2T-CHM13 annotation as a reference, we mapped all genes onto the Han1 genome and identified additional gene copies, generating a total of 60,708 putative genes, of which 20,003 are protein-coding. A comprehensive comparison between the genes revealed that 235 protein-coding genes were substantially different between the individuals, with frameshifts or truncations affecting the protein-coding sequence. Most of these were heterozygous variants in which one gene copy was unaffected. This represents the first gene-level comparison between two finished, annotated individual human genomes.
One-carbon metabolic enzymes are regulated during cell division and make distinct contributions to the metabolome and cell cycle progression in Saccharomyces cerevisiae
Authors: Hammer Staci E , Polymenis Michael 
Published: January 2023

Abstract
Enzymes of one-carbon (1C) metabolism play pivotal roles in proliferating cells. They are involved in the metabolism of amino acids, nucleotides, and lipids and the supply of all cellular methylations. However, there is limited information about how these enzymes are regulated during cell division and how cell cycle kinetics are affected in several loss-of-function mutants of 1C metabolism. Here, we report that the levels of the S. cerevisiae enzymes Ade17p and Cho2p, involved in the de novo synthesis of purines and phosphatidylcholine (PC), respectively, are cell cycle-regulated. Cells lacking Ade17p, Cho2p, or Shm2p (an enzyme that supplies 1C units from serine) have distinct alterations in size homeostasis and cell cycle kinetics. Loss of Ade17p leads to a specific delay at START, when cells commit to a new round of cell division, while loss of Shm2p has broader effects, reducing growth rate. Furthermore, the inability to synthesize PC de novo in cho2Δ cells delays START and reduces the coherence of nuclear elongation late in the cell cycle. Loss of Cho2p also leads to profound metabolite changes. Besides the expected changes in the lipidome, cho2Δ cells have reduced levels of amino acids, resembling cells shifted to poorer media. These results reveal the different ways that 1C metabolism allocates resources to affect cell proliferation at multiple cell cycle transitions.
Synaptogenesis: unmasking molecular mechanisms using Caenorhabditis elegans
Authors: Mizumoto Kota , Jin Yishi , Bessereau Jean-Louis 
Published: January 2023

Abstract
The nematode Caenorhabditis elegans is a research model organism particularly suited to the mechanistic understanding of synapse genesis in the nervous system. Armed with powerful genetics, knowledge of complete connectomics, and modern genomics, studies using C. elegans have unveiled multiple key regulators in the formation of a functional synapse. Importantly, many signaling networks display remarkable conservation throughout animals, underscoring the contributions of C. elegans research to advance the understanding of our brain. In this chapter, we will review up-to-date information of the contribution of C. elegans to the understanding of chemical synapses, from structure to molecules and to synaptic remodeling.
Context Matters: Health Sensitivity in the Daily Lives of Older Adults Living Through the COVID-19 Pandemic
Authors: Potter Sophie , Duezel Sandra , Demuth Ilja , Gerstorf Denis , Drewelies Johanna 
Published: January 2023

Abstract

Objectives
Throughout 2021, the coronavirus disease (COVID-19) pandemic caused renewed restrictions across Germany. Given the growing evidence that the pandemic negatively affects older adults’ health and well-being, this study investigated health sensitivity (emotional reactions to momentary health challenges) and its moderators (age, morbidity, perceived COVID-19 risks and worries) among older adults in their everyday lives during the second and third waves of the pandemic.

Methods
Multilevel models were applied to self-reported momentary health and affect data, collected 6 times per day across 7 consecutive days in 104 participants (Mage = 76.35; range: 67–88 years), assessed between April and June 2021 (~300,000 COVID-19 cases in Germany at the time).

Results
Health sensitivity was unrelated to age and lower with higher morbidity. Importantly, older adults showed higher health sensitivity in moments when they also perceived a greater risk of contracting COVID-19.

Discussion
Findings suggest that sociocontextual factors related to the pandemic modulate emotional reactions to momentary health challenges, thereby underscoring the consequences of COVID-19 for older adults’ emotional experiences.
Changes in Self-Perceptions of Aging Among Black and White Older Adults: The Role of Volunteering
Authors: Huo Meng , Kim Kyungmin , Haghighat Misha D 
Published: January 2023

Abstract

Objectives
Given the health consequences of self-perceptions of aging (SPA), understanding how SPA change among Black and White older adults may shed light on racial disparities in late-life health. The current study is the first to assess whether Black older adults exhibit less favorable patterns of change in SPA than White older adults. We also tested whether the salubrious effect of volunteering on SPA would be particularly salient among Black older adults.

Methods
A pooled sample of adults aged 50+ (N = 10,183; Black: n = 1,672, White: n = 8,511) from the Health and Retirement Study rated positive and negative SPA once every 4 years across 3 waves (2008/2010, 2012/2014, and 2016/2018). We assessed participants’ reports on volunteering status in each wave.

Results
Growth curve models revealed that positive SPA decreased over time whereas negative SPA increased. Black older adults reported more positive and less negative SPA at baseline and flatter time-related changes than their White counterparts. We found that volunteering was significantly associated with more positive and less negative SPA across waves, but this effect was only evident in White older adults.

Discussion
Findings revealed vulnerabilities in White older adults as they experience and perceive age-related changes but also identified volunteering as a way to uniquely protect them. More research is needed to refine our understanding of racial disparities in the United States and help tailor interventions intended to maximize benefits to older adults from diverse backgrounds.
Genistein Inhibits Clostridioides difficile Infection via Estrogen Receptors and Lysine-Deficient Protein Kinase 1
Authors: Xie Ying , Fontenot Lindsey , Estrada Andrea Chupina , Nelson Becca , Bullock Ashlen , Faull Kym F , Feng Hanping , Sun Mingjun , Koon Hon Wai 
Published: January 2023

Abstract

Background
Clostridioides difficile infection (CDI) is a debilitating nosocomial disease. Postmenopausal women may have an increased risk of CDI, suggesting estrogen influence. Soybean products contain a representative estrogenic isoflavone, genistein.

Methods
The anti-inflammatory and antiapoptotic effects of genistein were determined using primary human cells and fresh colonic tissues. The effects of oral genistein therapy among mice and hamsters were evaluated.

Results
Within 10 days of CDI, female c57BL/6J mice in a standard environment (regular diet) had a 50% survival rate, while those with estrogen depletion and in an isoflavone-free environment (soy-free diet) had a 25% survival rate. Oral genistein improved their 10-day survival rate to 100% on a regular diet and 75% in an isoflavone-free environment. Genistein reduced macrophage inflammatory protein-1α (MIP-1α) secretion in fresh human colonic tissues exposed to toxins. Genistein inhibited MIP-1α secretion in primary human peripheral blood mononuclear cells, abolished apoptosis and BCL-2–associated X (BAX) expression in human colonic epithelial cells, and activated lysine-deficient protein kinase 1 (WNK1) phosphorylation in both cell types. The anti-inflammatory and antiapoptotic effects of genistein were abolished by inhibiting estrogen receptors and WNK1.

Conclusions
Genistein reduces CDI disease activity by inhibiting proinflammatory cytokine expression and apoptosis via the estrogen receptor/G-protein estrogen receptor/WNK1 pathways.
Predicting the metabolizable energy and metabolizability of gross energy of conventional feedstuffs for Muscovy duck using in vitro digestion method
Authors: Wang Heng , Wang Xuyang , Zhan Yuchun , Peng Bin , Wang Wence , Yang Lin , Zhu Yongwen 
Published: January 2023

AbstractIn total, two experiments were conducted to evaluate the effectiveness of an in vitro digestion method for predicting the metabolizable energy (ME) and metabolizability of gross energy (ME/GE) values using in vitro digestible energy (IVDE) and the digestibility of gross energy (IVDE/GE) content, respectively, of conventional feedstuffs for Muscovy ducks. In experiment 1, the apparent metabolizable energy (AME), true metabolizable energy (TME), AME/GE, and TME/GE of eight-grain feedstuff samples (two corn samples, three sorghum samples, and three barley samples) and eight protein feedstuff samples (two soybean meal samples, three cottonseed meal samples, and three rapeseed meal samples) were determined by the tube-feeding method with six different ducks for each sample. In experiment 2, a computer-controlled simulated digestion system (CCSDS) contain simulated digestive fluid was used to determine the enzymatic hydrolysis energy value of feedstuffs, which was defined as IVDE in our study. The simulated gastric fluid containing pepsin and simulated small intestinal fluid containing amylase, trypsin, and chymotrypsin for the in vitro gastric and intestinal digestion, respectively. The IVDE and in vitro digestibility of GE (IVDE/GE) of 16 feedstuff samples were determined using the CCSDS with five replicates per sample. The results showed that the IVDE and IVDE/GE were positively correlated with ME and ME/GE of feedstuffs, respectively. The coefficient of determination of eight regression models in predicting ME (grain feedstuffs: AME = 1.050 × IVDE− 0.9293, TME = 1.032 × IVDE + 0.6478; protein feedstuffs: AME = 1.331 × IVDE− 6.685, TME = 1.269 × IVDE−3.490) and ME/GE (grain feedstuffs: AME/GE = 1.069 × IVDE/GE− 6.516, TME/GE = 1.068 × IVDE/GE + 0.7764; protein feedstuffs: AME/GE = 1.093 × IVDE/GE −19.21, TME/GE = 1.196 × IVDE/GE − 13.25) of feedstuffs for Muscovy ducks ranged from 0.8610 to 0.9921. The accuracy of the regression model was acceptable as the difference between measured and predicted ME and ME/GE values was less than 0.45 MJ/kg (100 kcal/kg) and 2.62% for 14 of the 16 feed samples, respectively. In conclusion, the in vitro digestion method can be used to predict the ME and ME/GE of conventional feedstuffs for Muscovy ducks with acceptable accuracy.
Maintaining Relevance in a Much-Changed World: Reforming WTO Dispute Settlement
Authors: Hughes Valerie 
Published: January 2023

ABSTRACT
The World Trade Organization (WTO) and its dispute settlement mechanism were established in 1995 to great acclaim. Both have seen much success: WTO membership expanded apace, and the WTO dispute settlement mechanism proved to be the most active state-to-state dispute settlement mechanism in history. However, in recent years, the WTO has come under increasing criticism as negotiations to expand and modernize WTO disciplines have produced limited results and dissatisfaction with the dispute settlement system on the part of the system’s most active user led to the paralysis of appellate review. Calls for WTO reform have become widespread. At the June 2022 Ministerial Conference, WTO members committed to work toward necessary reform, including by conducting discussions with a view to having a fully and well-functioning dispute settlement system in place by 2024. This is a tall order, given that long-standing efforts to agree on amendments to the dispute settlement system not only failed but also highlighted significant differences in members’ preferred approaches for resolving disputes. In addition, the legal processes required to implement the major change could take years. This paper identifies adjustments to the dispute settlement system that could lead to important efficiencies and that can be effected before the 2024 deadline arrives.
The role of multimodal salvage therapy in the management of recurrent adrenocortical carcinoma
Authors: Kijima Toshiki , Fukuda Shohei , Fukushima Hiroshi , Uehara Sho , Yasuda Yosuke , Yoshida Soichiro , Yokoyama Minato , Matsuoka Yoh , Saito Kazutaka , Fujii Yasuhisa 
Published: January 2023

Abstract

Background
Adrenocortical carcinoma is an aggressive tumor which often recurs despite apparent complete resection. This study assessed the long-term outcomes for patients with recurrent adrenocortical carcinoma after multimodal salvage therapy with chemotherapy, chemoradiotherapy and surgery.

Methods
We retrospectively reviewed medical records of patients who had a pathological diagnosis of adrenocortical carcinoma between 1996 and 2017. Kaplan–Meier curves were used to assess progression-free and cancer-specific survivals among all patients and cancer-specific survival among patients with tumor recurrence. Log-rank test was used to compare patient survivals by modality of salvage therapy (chemotherapy, chemoradiotherapy and chemotherapy/chemoradiotherapy plus surgery).

Results
Of 20 patients who underwent initial surgery, recurrence occurred in 14 (70%) with a median interval of 7.5 (range 1.0–12.6) months. Salvage therapy provided was chemotherapy only (n = 7), chemoradiotherapy (n = 2) and chemotherapy/chemoradiotherapy plus surgery (n = 5). Of the five patients who received salvage surgery, three underwent repeated resections. The potential benefit of multimodal salvage therapy was suggested in five patients (4 with chemotherapy/chemoradiotherapy plus surgery and 1 with chemoradiotherapy) who achieved durable disease control (cancer-specific survival from initial recurrence, 22–258 months). With a median follow-up of 25 months from recurrence, the 5-year cancer-specific survival rate was 58%. cancer-specific survival after recurrence was prolonged in patients with ≤ stage 3 disease, positive response to chemotherapy/chemoradiotherapy and salvage surgery.

Conclusions
Long-term disease control and survival could be achieved in highly selected patients with recurrent adrenocortical carcinoma using a multidisciplinary approach. Patients who had relatively limited recurrent sites and responded well to chemotherapy/chemoradiotherapy may be considered for salvage surgery on a case-by-case basis.
The conformation of glutenin polymers in wheat grain: some genetic and environmental factors associated with this important characteristic
Authors: Branlard Gérard , d’Orlando Angelina , Tahir Ayesha , Schmutz Marc , Rhazi Larbi , Faye Annie , Aussenac Thierry 
Published: January 2023

Abstract
In a previous study we used asymmetric-flow field-flow fractionation to determine the polymer mass (Mw), gyration radius (Rw) and the polydispersity index of glutenin polymers (GPs) in wheat (Triticum aestivum). Here, using the same multi-location trials (4 years, 11 locations, and 192 cultivars), we report the factors that are associated with the conformation (Conf) of the polymers, which is the slope of Log(Rw) versus a function of Log(Mw). We found that Conf varied between 0.285 and 0.740, it had low broad-sense heritability (H2=16.8), and it was significantly influenced by the temperature occurring over the last month of grain filling. Higher temperatures were found to increase Rw and the compactness and sphericity of GPs. Alleles for both high- and low-molecular-weight glutenin subunits had a significant influence on the Conf value. Assuming a Gaussian distribution for Mw, the number of polymers present in wheat grains was computed for different kernel weights and protein concentrations, and it was found to exceed 1012 GPs per grain. Using atomic force microscopy and cryo-TEM, images of GPs were obtained for the first time. Under higher average temperature, GPs became larger and more spherical and consequently less prone to rapid hydrolysis. We propose some orientations that could be aimed at potentially reducing the impact of numerous GPs on people suffering from non-celiac gluten sensitivity.
SQUAMOSA PROMOTER BINDING PROTEIN-LIKE 9 and 13 repressBLADE-ON-PETIOLE 1and2directly to promote adult leaf morphology in Arabidopsis
Authors: Hu Tieqiang , Manuela Darren , Xu Mingli 
Published: January 2023

AbstractThe juvenile-to-adult phase transition during vegetative development is a critical decision point in a plant’s life cycle. This transition is mediated by a decline in levels of miR156/157 and an increase in the activities of its direct targets, SQUAMOSA PROMOTER BINDING PROTEIN-LIKE (SPL) proteins. In Arabidopsis, the juvenile-to-adult transition is characterized by an increase in the length to width ratio of the leaf blade (a change in the distal region of a leaf), but what mediates this change in lamina shape is not known. Here, we show that ectopic expression of SPL9 and SPL13 produces enlarged and elongated leaves, resembling leaves from the blade-on-petiole1 (bop1) bop2 double mutant. The expression of BOP1/BOP2 is down-regulated in successive leaves, correlating with the amount of miR156 and antagonistic to the expression of SPL9 and SPL13 in leaves. SPL9 and SPL13 bind to the promoters of BOP1/BOP2 directly to repress their expression, resulting in delayed establishment of proliferative regions in leaves, which promotes more blade outgrowth (the distal region of a leaf) and suppresses petiole development (the proximal region of a leaf). Our results reveal a mechanism for leaf development along the proximal–distal axis, a heteroblastic character between juvenile leaves and adult leaves.
Comparative phyloproteomics identifies conserved plasmodesmal proteins
Authors: Johnston Matthew G , Breakspear Andrew , Samwald Sebastian , Zhang Dan , Papp Diana , Faulkner Christine , de Keijzer Jeroen 
Published: January 2023

AbstractPlasmodesmata are cytosolic bridges, lined by the plasma membrane and traversed by endoplasmic reticulum; plasmodesmata connect cells and tissues, and are critical for many aspects of plant biology. While plasmodesmata are notoriously difficult to extract, tissue fractionation and proteomic analyses can yield valuable knowledge of their composition. Here we have generated two novel proteomes to expand tissue and taxonomic representation of plasmodesmata: one from mature Arabidopsis leaves and one from the moss Physcomitrium patens, and leveraged these and existing data to perform a comparative analysis to identify evolutionarily conserved protein families that are associated with plasmodesmata. Thus, we identified β-1,3-glucanases, C2 lipid-binding proteins, and tetraspanins as core plasmodesmal components that probably serve as essential structural or functional components. Our approach has not only identified elements of a conserved plasmodesmal proteome, but also demonstrated the added power offered by comparative analysis for recalcitrant samples. Conserved plasmodesmal proteins establish a basis upon which ancient plasmodesmal function can be further investigated to determine the essential roles these structures play in multicellular organism physiology in the green lineages.
Scanning Transmission Ion Microscopy Time-of-Flight Spectroscopy Using 20 keV Helium Ions
Authors: Mousley Michael , Tabean Saba , Bouton Olivier , Hoang Quang H , Wirtz Tom , Eswara Santhana 
Published: January 2023

AbstractScanning transmission ion microscopy imaging was performed whilst using a delay-line detector to record the impact position and arrival time of transmitted ions or neutrals. The incident helium ion beam had an energy of 20 keV and the arrival time measurements were used to calculate the energy loss after transmission through the sample. The 5D dataset thus produced (2D position in the sample plane, 2D position in the detector plane, and energy) is analyzed by collection into energy spectra or images. It is demonstrated that ion energy loss maps can identify regions of identical materials in the sample plane. The behavior of the energy loss with respect to the scattering angle is calculated and these simulations agree with the experimentally measured results. This experiment demonstrates the capability of keV helium ions to be successfully used in energy loss imaging experiments. This is the first step in the development of keV scanning transmission ion microscopy energy loss techniques.