bluuebunny/crossref_metadata_2025_split huggingface dataset:
Notch signaling without the APH-2/nicastrin subunit of gamma secretase in Caenorhabditis elegans germline stem cells
Authors: Brinkley David M , Smith Karen C , Fink Emma C , Kwen Woohyun , Yoo Nina H , West Zachary , Sullivan Nora L , Farthing Alex S , Hale Valerie A , Goutte Caroline 
Published: May 2024

Abstract
The final step in Notch signaling activation is the transmembrane cleavage of Notch receptor by γ secretase. Thus far, genetic and biochemical evidence indicates that four subunits are essential for γ secretase activity in vivo: presenilin (the catalytic core), APH-1, PEN-2, and APH-2/nicastrin. Although some γ secretase activity has been detected in APH-2/nicastrin-deficient mammalian cell lines, the lack of biological relevance for this activity has left the quaternary γ secretase model unchallenged. Here, we provide the first example of in vivo Notch signal transduction without APH-2/nicastrin. The surprising dispensability of APH-2/nicastrin is observed in Caenorhabditis elegans germline stem cells (GSCs) and contrasts with its essential role in previously described C. elegans Notch signaling events. Depletion of GLP-1/Notch, presenilin, APH-1, or PEN-2 causes a striking loss of GSCs. In contrast, aph-2/nicastrin mutants maintain GSCs and exhibit robust and localized expression of the downstream Notch target sygl-1. Interestingly, APH-2/nicastrin is normally expressed in GSCs and becomes essential under conditions of compromised Notch function. Further insight is provided by reconstituting the C. elegans γ secretase complex in yeast, where we find that APH-2/nicastrin increases but is not essential for γ secretase activity. Together, our results are most consistent with a revised model of γ secretase in which the APH-2/nicastrin subunit has a modulatory, rather than obligatory role. We propose that a trimeric presenilin-APH-1-PEN-2 γ secretase complex can provide a low level of γ secretase activity, and that cellular context determines whether or not APH-2/nicastrin is essential for effective Notch signal transduction.
A theory of optimal convex regularization for low-dimensional recovery
Authors: Traonmilin Yann , Gribonval Rémi , Vaiter Samuel 
Published: May 2024

Abstract
We consider the problem of recovering elements of a low-dimensional model from under-determined linear measurements. To perform recovery, we consider the minimization of a convex regularizer subject to a data fit constraint. Given a model, we ask ourselves what is the ‘best’ convex regularizer to perform its recovery. To answer this question, we define an optimal regularizer as a function that maximizes a compliance measure with respect to the model. We introduce and study several notions of compliance. We give analytical expressions for compliance measures based on the best-known recovery guarantees with the restricted isometry property. These expressions permit to show the optimality of the $\ell ^{1}$-norm for sparse recovery and of the nuclear norm for low-rank matrix recovery for these compliance measures. We also investigate the construction of an optimal convex regularizer using the examples of sparsity in levels and of sparse plus low-rank models.
Microbiome processing of organic nitrogen input supports growth and cyanotoxin production of Microcystis aeruginosa cultures
Authors: Li Wei , Baliu-Rodriguez David , Premathilaka Sanduni H , Thenuwara Sharmila I , Kimbrel Jeffrey A , Samo Ty J , Ramon Christina , Kiledal Erik Anders , Rivera Sara R , Kharbush Jenan , Isailovic Dragan , Weber Peter K , Dick Gregory J , Mayali Xavier 
Published: May 2024

Abstract
Nutrient-induced blooms of the globally abundant freshwater toxic cyanobacterium Microcystis cause worldwide public and ecosystem health concerns. The response of Microcystis growth and toxin production to new and recycled nitrogen (N) inputs and the impact of heterotrophic bacteria in the Microcystis phycosphere on these processes are not well understood. Here, using microbiome transplant experiments, cyanotoxin analysis, and nanometer-scale stable isotope probing to measure N incorporation and exchange at single cell resolution, we monitored the growth, cyanotoxin production, and microbiome community structure of several Microcystis strains grown on amino acids or proteins as the sole N source. We demonstrate that the type of organic N available shaped the microbial community associated with Microcystis, and external organic N input led to decreased bacterial colonization of Microcystis colonies. Our data also suggest that certain Microcystis strains could directly uptake amino acids, but with lower rates than heterotrophic bacteria. Toxin analysis showed that biomass-specific microcystin production was not impacted by N source (i.e. nitrate, amino acids, or protein) but rather by total N availability. Single-cell isotope incorporation revealed that some bacterial communities competed with Microcystis for organic N, but other communities promoted increased N uptake by Microcystis, likely through ammonification or organic N modification. Our laboratory culture data suggest that organic N input could support Microcystis blooms and toxin production in nature, and Microcystis-associated microbial communities likely play critical roles in this process by influencing cyanobacterial succession through either decreasing (via competition) or increasing (via biotransformation) N availability, especially under inorganic N scarcity.
Effects of high doses of zearalenone on some antioxidant enzymes and locomotion of Tenebrio molitor larvae (Coleoptera: Tenebrionidae)
Authors: Janković-Tomanić Milena , Petković Branka , Vranković Jelena S , Perić-Mataruga Vesna 
Published: May 2024

Abstract
The mealworm Tenebrio molitor L. (Coleoptera: Tenebrionidae) feeds on wheat bran and is considered both a pest and an edible insect. Its larvae contain proteins and essential amino acids, fats, and minerals, making them suitable for animal and human consumption. Zearalenone (ZEA) is the mycotoxin most commonly associated with Fusarium spp. It is found in cereals and cereal products, so their consumption is a major risk for mycotoxin contamination. One of the most important effects of ZEA is the induction of oxidative stress, which leads to physiological and behavioral changes. This study deals with the effects of high doses of ZEA (10 and 20 mg/kg) on survival, molting, growth, weight gain, activity of antioxidant enzymes superoxide dismutase (SOD) and glutathione S-transferase (GST), and locomotion of mealworm larvae. Both doses of ZEA were found to (i) have no effect on survival, (ii) increase molting frequency, SOD, and GST activity, and (iii) decrease body weight and locomotion, with more pronounced changes at 20 mg/kg. These results indicated the susceptibility of T. molitor larvae to high doses of ZEA in feed.
RE: Expert range maps of global mammal distributions harmonised to three taxonomic authorities
Authors: Arbogast Brian S , Kerhoulas Nicholas J 
Published: May 2024

Abstract
In a recent paper titled Expert range maps of global mammal distributions harmonised to three taxonomic authorities, Marsh et al. (2022) introduced a series of new geographic range maps for all extant species of mammals and made these maps available on the Map of Life (MoL) website (www.mol.org). The title of the paper and inclusion of over 140 prominent mammalogists and biogeographers as coauthors strongly suggested that these new range maps were carefully vetted. However, when examining the maps of Marsh et al. (2022) on the MoL web platform, we found a variety of serious problems, including, but not limited to: range exaggerations (inclusion of substantial geographic areas not represented by specimen records or verified observations); range maps that are geographically shifted so that species are shown as occurring in areas in which they do not, and not occurring in areas in which they do (and in some cases, these new maps do not even encompass the type locality of a species); range maps that simply omit peripheral populations of conservation concern; and range maps for fully marine mammals (i.e., those that do not spend any time on land) that include large swaths of both insular and continental landmasses. Overall, we evaluated the new “expert” mammal range maps on the MoL platform for 78 species (retrieved between 31 March 2022 and 1 April 2023) and show that there are serious, systemic problems with these maps, and that these problems are both geographically and taxonomically widespread. As such, we caution researchers to carefully review and evaluate the range maps of Marsh et al. (2022) on the MoL before using them for any research purpose—including conservation, biogeographical, and macroecological analyses of mammals.
Response to Arbogast and Kerhoulas
Authors: Marsh Charles J , Sica Yanina V , Upham Nathan S , Jetz Walter 
Published: May 2024

Abstract
We welcome feedback on the range maps published in Marsh et al. (2022) where it constructively improves our knowledge on species distributions. Unfortunately, we are concerned that criticisms raised by Arbogast and Kerhoulas are steps backward, not forward, particularly as they did not access the original range map data of Marsh et al. (2022). We stress that evaluating range maps using Global Biodiversity Information Facility data without the necessary quality control and filtering will lead to flawed interpretations—using the same approach, an even greater proportion, &gt;99.5%, of IUCN mammal range maps would fail to meet their expectations. We take this opportunity to highlight the fine-scale inaccuracies, scale limitations, and range map variance that are expected across all expert range map sources and that any researcher should consider during any analysis. Finally, we again announce the availability of an online tool for providing annotations and proposing adjustments to range maps, and suggest this as a more appropriate forum for constructively and transparently improving range maps.
Mosquitoes do not influence Cotton Mouse (Peromyscus gossypinus) giving-up densities
Authors: Morris Gail , Conner L Mike 
Published: May 2024

Abstract
It is commonly recognized that predation and the risk of predation can have profound effects on behaviors and population ecology of prey. Comparatively, little attention has been paid to the trade-offs hosts make to manage the risk of parasitism, but there is evidence that hosts make behavioral trade-offs to avoid parasitism in ways that resemble those made by prey animals under the risk of predation. Mosquitoes are common hematophagous ectoparasites which parasitize a wide range of vertebrates, resulting in blood loss, distraction, and disease transmission. Many hosts engage in defensive behaviors to repel or kill mosquitoes and these behaviors likely come at the expense of activities such as foraging and vigilance for predators. We placed a mosquito attractant (BG-Sweetscent) and repellant (allethrin) near artificial foraging patches in areas where mosquitoes were common and measured the amount of grain left after a night of foraging (giving-up density) to investigate whether mosquitoes influenced Cotton Mouse (Peromyscus gossypinus) foraging. We predicted that in patches with mosquito attractants, mosquito harassment would cause mice to engage in defensive behaviors which would distract or deter them from foraging, resulting in less grain consumption relative to control patches. Conversely, we predicted that in mosquito-repellent patches, mice would experience less harassment, resulting in more grain consumption. Indoor arena trials found no evidence that the mosquito treatments influenced cotton mouse behavior in the absence of mosquitoes. However, we found no evidence that mosquito treatments affected giving-up densities.
Macromolecular tool box to elucidate CLAVATA3/EMBRYO SURROUNDING REGION-RELATED–RLK binding, signaling, and downstream effects
Authors: Narasimhan Madhumitha , Jahnke Nina , Kallert Felix , Bahafid Elmehdi , Böhmer Franziska , Hartmann Laura , Simon Rüdiger 
Published: May 2024

Abstract
Plant peptides communicate by binding to a large family of receptor-like kinases (RLKs), and they share a conserved binding mechanism, which may account for their promiscuous interaction with several RLKs. In order to understand the in vivo binding specificity of the CLAVATA3/EMBRYO SURROUNDING REGION-RELATED peptide family in Arabidopsis, we have developed a novel set of CLAVATA3 (CLV3)-based peptide tools. After carefully evaluating the CLE peptide binding characteristics, using solid phase synthesis process, we modified the CLV3 peptide and attached a fluorophore and a photoactivable side group. We observed that the labeled CLV3 shows binding specificity within the CLAVATA1 clade of RLKs while avoiding the distantly related PEP RECEPTOR clade, thus resolving the contradictory results obtained previously by many in vitro methods. Furthermore, we observed that the RLK-bound CLV3 undergoes clathrin-mediated endocytosis and is trafficked to the vacuole via ARA7 (a Rab GTPase)-labeled endosomes. Additionally, modifying CLV3 for light-controlled activation enabled spatial and temporal control over CLE signaling. Hence, our CLV3 macromolecular toolbox can be used to study rapid cell specific down-stream effects. Given the conserved binding properties, in the future our toolbox can also be used as a template to modify other CLE peptides.
Polycomb proteins RING1A/B promote H2A monoubiquitination to regulate female gametophyte development in Arabidopsis
Authors: Lv Yanfang , Li Jian , Wang Zheng , Liu Yue , Jiang Yili , Li Yanzhuo , Lv Zhaopeng , Huang Xiaoyi , Peng Xiongbo , Cao Ying , Yang Hongchun 
Published: May 2024

Abstract
A functional female gametophyte is the basis of successful sexual reproduction in flowering plants. During female gametophyte development, the megaspore mother cell (MMC), which differentiates from a single subepidermal somatic cell in the nucellus, undergoes meiosis to produce four megaspores; only the one at the chalazal end, referred to as the functional megaspore (FM), then undergoes three rounds of mitosis and develops into a mature embryo sac. Here, we report that RING1A and RING1B (RING1A/B), two functionally redundant Polycomb proteins in Arabidopsis, are critical for female gametophyte development. Mutations of RING1A/B resulted in defects in the specification of the MMC and the FM, and in the subsequent mitosis of the FM, thereby leading to aborted ovules. Detailed analysis revealed that several genes essential for female gametophyte development were ectopically expressed in the ring1a ring1b mutant, including Argonaute (AGO) family genes and critical transcription factors. Furthermore, RING1A/B bound to some of these genes to promote H2A monoubiquitination (H2Aub). Taken together, our study shows that RING1A/B promote H2Aub modification at key genes for female gametophyte development, suppressing their expression to ensure that the development progresses correctly.
Identification and in vitro characterization of UDP-GlcNAc-RNA cap-modifying and decapping enzymes
Authors: Weber Frederik , Motzkus Nikolas Alexander , Brandl Leona , Möhler Marvin , Alempijevic Andrijana , Jäschke Andres 
Published: May 2024

Abstract
In recent years, several noncanonical RNA caps derived from cofactors and metabolites have been identified. Purine-containing RNA caps have been extensively studied, with multiple decapping enzymes identified and efficient capture and sequencing protocols developed for nicotinamide adenine dinucleotide (NAD)-RNA, which allowed for a stepwise elucidation of capping functions. Despite being identified as an abundant noncanonical RNA-cap, UDP-sugar-capped RNA remains poorly understood, which is partly due to its complex in vitro preparation. Here, we describe a scalable synthesis of sugar-capped uridine-guanosine dinucleotides from readily available protected building blocks and their enzymatic conversion into several cell wall precursor-capped dinucleotides. We employed these capped dinucleotides in T7 RNA polymerase-catalyzed in vitro transcription reactions to efficiently generate RNAs capped with uridine diphosphate N-acetylglucosamine (UDP-GlcNAc), its N-azidoacetyl derivative UDP-GlcNAz, and various cell wall precursors. We furthermore identified four enzymes capable of processing UDP-GlcNAc-capped RNA in vitro: MurA, MurB and MurC from Escherichia coli can sequentially modify the sugar-cap structure and were used to introduce a bioorthogonal, clickable moiety, and the human Nudix hydrolase Nudt5 was shown to efficiently decap UDP-GlcNAc-RNA. Our findings underscore the importance of efficient synthetic methods for capped model RNAs. Additionally, we provide useful enzymatic tools that could be utilized in the development and application of UDP-GlcNAc capture and sequencing protocols. Such protocols are essential for deepening our understanding of the widespread yet enigmatic GlcNAc modification of RNA and its physiological significance.
A neural tract-inspired conduit for facile, on-demand biopsy of glioblastoma
Authors: Betancur Martha I , Case Ayden , Ilich Ekaterina , Mehta Nalini , Meehan Sean , Pogrebivsky Sabrina , Keir Stephen T , Stevenson Kevin , Brahma Barun , Gregory Simon , Chen Wei , Ashley David M , Bellamkonda Ravi , Mokarram Nassir 
Published: May 2024

Abstract

Background
A major hurdle to effectively treating glioblastoma (GBM) patients is the lack of longitudinal information about tumor progression, evolution, and treatment response.

Methods
In this study, we report the use of a neural tract-inspired conduit containing aligned polymeric nanofibers (i.e., an aligned nanofiber device) to enable on-demand access to GBM tumors in 2 rodent models. Depending on the experiment, a humanized U87MG xenograft and/or F98-GFP+ syngeneic rat tumor model was chosen to test the safety and functionality of the device in providing continuous sampling access to the tumor and its microenvironment.

Results
The aligned nanofiber device was safe and provided a high quantity of quality genomic materials suitable for omics analyses and yielded a sufficient number of live cells for in vitro expansion and screening. Transcriptomic and genomic analyses demonstrated continuity between material extracted from the device and that of the primary, intracortical tumor (in the in vivo model).

Conclusions
The results establish the potential of this neural tract-inspired, aligned nanofiber device as an on-demand, safe, and minimally invasive access point, thus enabling rapid, high-throughput, longitudinal assessment of tumor and its microenvironment, ultimately leading to more informed clinical treatment strategies.
Trimethoprim-Sulfamethoxazole Plus Azithromycin to Prevent Malaria and Sexually Transmitted Infections in Pregnant Women With HIV (PREMISE): A Randomized, Double-Masked, Placebo-Controlled, Phase IIB Clinical Trial
Authors: Dionne Jodie A , Anchang-Kimbi Judith , Hao Jiaying , Long Dustin , Apinjoh Tobias , Tih Pius , Mbah Rahel , Ngah Edward Ndze , Juliano Jonathan J , Kahn Mauricio , Bruxvoort Katia , Van Der Pol Barbara , Tita Alan T N , Marrazzo Jeanne , Achidi Eric 
Published: May 2024

Abstract

Background
This trial tested the effectiveness of a novel regimen to prevent malaria and sexually transmitted infections (STIs) among pregnant women with HIV in Cameroon. Our hypothesis was that the addition of azithromycin (AZ) to standard daily trimethoprim-sulfamethoxazole (TMP-SMX) prophylaxis would reduce malaria and STI infection rates at delivery.

Methods
Pregnant women with HIV at gestational age &lt;28 weeks were randomized to adjunctive monthly oral AZ 1 g daily or placebo for 3 days and both groups received daily standard oral TMP-SMX through delivery. Primary outcomes were (1) positive peripheral malaria infection by microscopy or polymerase chain reaction and (2) composite bacterial genital STI (Chlamydia trachomatis, Neisseria gonorrhoeae, or syphilis) at delivery. Relative risk and 95% confidence intervals were estimated using 2 × 2 tables with significance as P &lt; .05.

Results
Pregnant women with HIV (n = 308) were enrolled between March 2018 and August 2020: 155 women were randomized to TMP-SMX-AZ and 153 women to TMP-SMX-placebo. Groups were similar at baseline and loss to follow up was 3.2%. There was no difference in the proportion with malaria (16.3% in TMP-SMX-AZ vs 13.2% in TMP-SMX; relative risk, 1.24 [95% confidence interval, .71-2.16]) or STI at delivery (4.2% in TMP-SMX-AZ vs 5.8% in TMP-SMX; relative risk, 0.72 [95% confidence interval, .26-2.03]). Adverse birth outcomes were not significantly different, albeit lower in the TMP-SMX-AZ arm (preterm delivery 6.7% vs 10.7% [P = .3]; low birthweight 3.4% vs 5.4% [P = .6]).

Conclusions
The addition of monthly azithromycin to daily TMP-SMX prophylaxis in pregnant women living with HIV in Cameroon did not reduce the risk of malaria or bacterial STI at delivery.
Policy variation in the external evaluation of research for tenure at U.S. universities
Authors: Hannon Lance , Bergey Meredith 
Published: May 2024

Abstract
There is a robust literature documenting differences in peer review processes for scholarly outlets. Knowledge of this variability has provoked thoughtful debate about the best approach for promoting rigor and innovation in scientific research (e.g. single-blind vs. double-blind review, or more recently, double-blind vs. open review). We aim to expand this conversation to external peer review processes specified in rank and tenure guidelines. We qualitatively analyze a corpus of publicly available rank and tenure procedures at research-intensive universities in the United States. Results indicate significant variation in (1) the required minimum and maximum number of external reviews, (2) the candidate’s role in the reviewer selection process, (3) the level of ensured anonymity for reviewers, and (4) attention to potential conflict of interest scenarios. We argue that many of the debates about best practices in research evaluation for journals and funding agencies are also relevant for rank and tenure procedures. Moreover, rank and tenure policies may be subject to unique tensions, such as cases where external reviews are formally cast as disinterested assessments by referees but informally understood as letters of recommendation by sponsors. We discuss the relevance of our findings for existing work on the perceived clarity of evaluation criteria—especially how guideline ambiguity can be linked to inequality and how labor issues can conflict with idealized assessment principles.