bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evolution of Human-Specific Alleles Protecting Cognitive Function of Grandmothers
Authors: Saha Sudeshna , Khan Naazneen , Comi Troy , Verhagen Andrea , Sasmal Aniruddha , Diaz Sandra , Yu Hai , Chen Xi , Akey Joshua M , Frank Martin , Gagneux Pascal , Varki Ajit 
Published: July 2022

Abstract
The myelomonocytic receptor CD33 (Siglec-3) inhibits innate immune reactivity by extracellular V-set domain recognition of sialic acid (Sia)-containing “self-associated molecular patterns” (SAMPs). We earlier showed that V-set domain-deficient CD33-variant allele, protective against late-onset Alzheimer’s Disease (LOAD), is derived and specific to the hominin lineage. We now report multiple hominin-specific CD33 V-set domain mutations. Due to hominin-specific, fixed loss-of-function mutation in the CMAH gene, humans lack N-glycolylneuraminic acid (Neu5Gc), the preferred Sia-ligand of ancestral CD33. Mutational analysis and molecular dynamics (MD)-simulations indicate that fixed change in amino acid 21 of hominin V-set domain and conformational changes related to His45 corrected for Neu5Gc-loss by switching to N-acetylneuraminic acid (Neu5Ac)-recognition. We show that human-specific pathogens Neisseria gonorrhoeae and Group B Streptococcus selectively bind human CD33 (huCD33) as part of immune-evasive molecular mimicry of host SAMPs and that this binding is significantly impacted by amino acid 21 modification. In addition to LOAD-protective CD33 alleles, humans harbor derived, population-universal, cognition-protective variants at several other loci. Interestingly, 11 of 13 SNPs in these human genes (including CD33) are not shared by genomes of archaic hominins: Neanderthals and Denisovans. We present a plausible evolutionary scenario to compile, correlate, and comprehend existing knowledge about huCD33-evolution and suggest that grandmothering emerged in humans.
Functional significance of mouse seminal vesicle sulfhydryl oxidase on sperm capacitationin vitro
Authors: Balu Rubhadevi , Ramachandran Shiyam Sundar , Mathimaran Amala , Jeyaraman Jeyakanthan , Paramasivam Sudhakar Gandhi 
Published: July 2022

AbstractDuring ejaculation, cauda epididymal spermatozoa are suspended in a protein-rich solution of seminal plasma, which is composed of proteins mostly secreted from the seminal vesicle. These seminal proteins interact with the sperm cells and bring about changes in their physiology, so that they can become capacitated in order for the fertilization to take place. Sulfhydryl oxidase (SOX) is a member of the QSOX family and its expression is found to be high in the seminal vesicle secretion (SVS) of mouse. Previously, it has been reported to cross-link thiol-containing amino acids among major SVS proteins. However, its role in male reproduction is unclear. In this study, we determined the role of SOX on epididymal sperm maturation and also disclosed the binding effect of SOX on the sperm fertilizing ability in vitro. In order to achieve the above two objectives, we constructed a Sox clone (1.7 kb) using a pET-30a vector. His-tagged recombinant Sox was overexpressed in Shuffle Escherichia coli cells and purified using His-Trap column affinity chromatography along with hydrophobic interaction chromatography. The purified SOX was confirmed by western blot analysis and by its activity with DTT as a substrate. Results obtained from immunocytochemical staining clearly indicated that SOX possesses a binding site on the sperm acrosome. The influence of SOX on oxidation of sperm sulfhydryl to disulfides during epididymal sperm maturation was evaluated by a thiol-labeling agent, mBBr. The SOX protein binds onto the sperm cells and increases their progressive motility. The effect of SOX binding on reducing the [Ca2+]i concentration in the sperm head was determined using a calcium probe, Fluo-3 AM. The inhibitory influence of SOX on the sperm acrosome reaction was shown by using calcium ionophore A32187 to induce the acrosome reaction. The acrosome-reacted sperm were examined by staining with FITC-conjugated Arachis hypogaea (peanut) lectin. Furthermore, immunocytochemical analysis revealed that SOX remains bound to the sperm cells in the uterus but disappears in the oviduct during their transit in the female reproductive tract. The results from the above experiment revealed that SOX binding onto the sperm acrosome prevents sperm capacitation by affecting the [Ca2+]i concentration in the sperm head and the ionophore-induced acrosome reaction. Thus, the binding of SOX onto the sperm acrosome may possibly serve as a decapacitation factor in the uterus to prevent premature capacitation and acrosome reaction, thus preserving their fertilizing ability.
Assessing the morphological impacts of long-term harvesting in intertidal gastropods using historical data and morphometric tools
Authors: Doyle Darragh , Frias João , Gammell Martin P , Lynch Michael , Nash Roisin 
Published: July 2022

ABSTRACTSize-selective harvesting of intertidal molluscs is a common practice. However, the effects of long-term traditional harvesting remain unclear. Changes in mean shell size are generally taken as evidence of changes in harvesting intensity. However, mean shell size is also influenced by environmental pressures, which may confound the analysis of size variation over time. In this study, we apply geometric morphometrics to historical data from two shell middens, in an attempt to classify Littorina littorea shells to their environmental origins, prior to carrying out shell size analysis. Using this method, shell shape was found to be consistent within and between the midden sites. Based on comparison with modern populations from shores of known wave exposure, the midden shells were found to be more consistent with sheltered shores, and to differ most from the very exposed shore sites, the latter of which are located adjacent to the midden remains. The mean shell size was significantly smaller in the more recent midden site. We hypothesize this reduction is caused by an increase in harvesting intensity over this period. It is also possible, given the very slight reduction in shell size, coupled with certain life-history traits of L. littorea, that the change in shell size was caused by slight differences in environmental conditions. The use of midden shells and morphometrics has the potential to provide an insight into previous environmental conditions and past harvesting practices, which may be used to inform current harvesting practices.
Climate change is predicted to reduce sympatry among North American wood-warblers
Authors: Pham Cody H , Price J Jordan , Tallant Jason M , Karowe David N 
Published: July 2022

Abstract
Anthropogenic climate change will dramatically alter species distributions. The rate and magnitude of range shifts, however, will differ among taxa, resulting in altered patterns of co-occurrence and interspecific interactions. We examined potential climate-mediated breeding range shifts among North American wood-warblers (Parulidae), a speciose avian family likely to be especially impacted by such changes due to high levels of interspecific competition and hybridization. We used publicly available species distribution model (SDM) range outputs to compare current ranges and patterns of sympatry among warbler species to future ranges and sympatry under 1.5°C, 2.0°C, and 3.0°C of average global warming. Range overlap among species and number of sympatric species are expected to decrease significantly in future warming scenarios, and unequal range shifts will alter the composition of warbler communities. On average, climate change will result in net decreases in the local species diversity; each warbler species is predicted to gain sympatry with approximately 1 new species and lose sympatry with approximately 2 species. Climate-mediated changes are predicted to differ among warblers in different regions of North America, with greatest impacts on eastern and boreal forest species. Our findings suggest that climate change will alter the diversity of wood-warbler communities during this century. Targeted monitoring of these changing interspecific relationships, especially for antagonistic interactions or hybridization between newly sympatric species, will be crucial for prioritizing particular species and regions in future conservation or management efforts.
Clinical training within an Indigenous community: a qualitative description of pediatric residents’ learning experiences
Authors: Waldner Richelle , Baydala Lola , Tremblay Melissa , Pynoo Emily , Dreise Heather 
Published: July 2022

Abstract

Objectives
Indigenous children and families experience inequities across health domains. Calls to action from the Truth and Reconciliation Commission of Canada and the Indigenous Physicians Association of Canada have highlighted the need for medical professionals to better understand these inequities and improve the provision of culturally safe services through collaboration between Indigenous communities and medical residency programs. There are currently no published evaluations of clinical training for Canadian medical residents within Indigenous communities. The current study was conducted at an on-reserve pediatric outreach clinic (Maskwacis Pediatric Outreach Clinic; MPOC).

Methods
From the perspectives of pediatric residents, the researchers explored the impacts of attending MPOC during resident training. Residents completed anonymous surveys over an 18-month period that addressed patient and caregiver encounters, the value of MPOC on resident training, significant pediatric health issues in the community, and limitations of MPOC in contributing to training. Seven residents participated in a focus group that expanded upon survey results.

Results
Thirty-four surveys were completed. Responses reflected an enhanced understanding of social, environmental, and systemic contributors to health issues, and learning regarding the complexity of circumstances that Indigenous children and families face. Focus group results were organized into the impacts of MPOC on (1) residents and (2) patients, with several sub-categories.

Conclusions
Findings suggest that direct clinical exposure to Indigenous child health issues is a valuable educational experience for pediatric residents. The importance of strength-based approaches to educating medical residents regarding the social determinants of health and colonial contexts of Indigenous health disparities is also identified.
Mothers’ experiences and perceptions of their child’s weaning process from tube feeding within a multidisciplinary Paediatric Feeding Program
Authors: Cipolla Josie , Reeves-Latour Jonathan , Ramsay Maria , Li Patricia 
Published: July 2022

Abstract

Objectives
Previous studies have described the negative impact that tube feeding of children with complex chronic diseases has on the caregivers’ emotions, relationships and daily life. It is unclear whether these negative experiences persist or change during and after the weaning process. We sought to explore mothers’ experiences and perceptions of their child being weaned off tube feeding within a Paediatric Feeding Program (PFP).

Methods
We conducted a qualitative study using semi-structured interviews with mothers whose children &lt;4 years old had experienced feeding tube weaning within an outpatient, family-centred, telemedicine-supported PFP. The transcripts were analyzed using thematic analysis.

Results
We conducted 9 interviews with mothers of children (n = 10) in the PFP at which point data saturation was achieved. Three main themes emerged: a) the initial emotional toll on mothers stemming from fear of perceived adverse consequences of decreasing tube feeds and uncertainty surrounding efficacy of weaning; b) achievement of weaning via a family-centered approach through gaining trust, close contact, and collaboration with the team; and c) attainment of mothers’ expectations of family life through transformed relationships and social activities. A positive evolution of emotions was observed, attributable to the support of the PFP.

Conclusions
These experiences suggest that our outpatient weaning program had a positive impact on the stress, fear, and relational challenges that mothers reported before and during initial tube weaning. These findings highlight potential areas of discussion with families at multiple stages of the child’s tube feeding experience, to help normalize emotions for families and support coping strategies.
Gödel’s Disjunctive Argument
Authors: Wrigley Wesley 
Published: July 2022

AbstractGödel argued that the incompleteness theorems entail that the mind is not a machine, or that certain arithmetical propositions are absolutely undecidable. His view was that the mind is not a machine, and that no arithmetical propositions are absolutely undecidable. I argue that his position presupposes that the idealized mathematician has an ability which I call the recursive-ordinal recognition ability. I show that we have this ability if, and only if, there are no absolutely undecidable arithmetical propositions. I argue that there are such propositions, but that no recognizable example of one can be identified, even in principle.
Brassinosteroid signaling restricts root lignification by antagonizing SHORT-ROOT function in Arabidopsis
Authors: Li Meng , Li Pengxue , Wang Chunhua , Xu Huimin , Wang Mengxue , Wang Yanli , Niu Xufang , Xu Mengyuan , Wang Hong , Qin Yaxin , Tang Wenqiang , Bai Mingyi , Wang Wenfei , Wu Shuang 
Published: July 2022

Abstract
Cell wall lignification is a key step in forming functional endodermis and protoxylem (PX) in plant roots. Lignified casparian strips (CS) in endodermis and tracheary elements of PX are essential for selective absorption and transport of water and nutrients. Although multiple key regulators of CS and PX have been identified, the spatial information that drives the developmental shift to root lignification remains unknown. Here, we found that brassinosteroid (BR) signaling plays a key role in inhibiting root lignification in the root elongation zone. The inhibitory activity of BR signaling occurs partially through the direct binding of BRASSINAZOLE-RESISTANT 1 (BZR1) to SHORT-ROOT (SHR), repressing the SHR-mediated activation of downstream genes that are involved in root lignification. Upon entering the mature root zone, BR signaling declines rapidly, which releases SHR activity and initiates root lignification. Our results provide a mechanistic view of the developmental transition to cell wall lignification in Arabidopsis thaliana roots.
A KARRIKIN INSENSITIVE2 paralog in lettuce mediates highly sensitive germination responses to karrikinolide
Authors: Martinez Stephanie E , Conn Caitlin E , Guercio Angelica M , Sepulveda Claudia , Fiscus Christopher J , Koenig Daniel , Shabek Nitzan , Nelson David C 
Published: July 2022

Abstract
Karrikins (KARs) are chemicals in smoke that can enhance germination of many plants. Lettuce (Lactuca sativa) cv. Grand Rapids germinates in response to nanomolar karrikinolide (KAR1). Lettuce is much less responsive to KAR2 or a mixture of synthetic strigolactone analogs, rac-GR24. We investigated the molecular basis of selective and sensitive KAR1 perception in lettuce. The lettuce genome contains two copies of KARRIKIN INSENSITIVE2 (KAI2), which in Arabidopsis (Arabidopsis thaliana) encodes a receptor that is required for KAR responses. LsKAI2b is more highly expressed than LsKAI2a in dry achenes and during early stages of imbibition. Through cross-species complementation assays in Arabidopsis, we found that an LsKAI2b transgene confers robust responses to KAR1, but LsKAI2a does not. Therefore, LsKAI2b likely mediates KAR1 responses in lettuce. We compared homology models of KAI2 proteins from lettuce and a fire-follower, whispering bells (Emmenanthe penduliflora). This identified pocket residues 96, 124, 139, and 161 as candidates that influence the ligand specificity of KAI2. Further support for the importance of these residues was found through a broader comparison of pocket residues among 281 KAI2 proteins from 184 asterid species. Almost all KAI2 proteins had either Tyr or Phe identity at position 124. Genes encoding Y124-type KAI2 are more broadly distributed in asterids than in F124-type KAI2. Substitutions at residues 96, 124, 139, and 161 in Arabidopsis KAI2 produced a broad array of responses to KAR1, KAR2, and rac-GR24. This suggests that the diverse ligand preferences observed among KAI2 proteins in plants could have evolved through relatively few mutations.
Was John Donne a Catholic?: Conversion, Conformity, and Early Modern English Confessional Identities
Authors: Morrissey Mary 
Published: July 2022

Abstract
John Donne is usually treated as a convert from Roman Catholicism, and he is often said to have been brought up as a recusant Catholic. This article challenges these assumptions about Donne’s background, showing them to rely too heavily on the surviving records of his mother’s family. By considering the surviving evidence on other members of Donne’s family (his father and stepfather in particular), and by comparing Donne’s choices with those of other young men from similar families, we can understand Donne’s religious identity as one shaped by conformity rather than conversion. This does not mean that Donne ‘merely’ conformed without conscientiously choosing the teaching (and the teaching authority) of the Church of England over that of the Roman Catholic Church. It is to argue that, when an adult Donne described himself as someone who had been a member of the Church of England since his baptism, he cannot therefore be said to have converted to Protestantism. Donne decided on his religious allegiance when he was of an age to make that choice, and his decision is not recorded by anyone other than himself because it was unremarkable and legal.
Belief Convergence under Misspecified Learning: A Martingale Approach
Authors: Frick Mira , Iijima Ryota , Ishii Yuhta 
Published: July 2022

Abstract
We present an approach to analyse learning outcomes in a broad class of misspecified environments, spanning both single-agent and social learning. We introduce a novel “prediction accuracy” order over subjective models and observe that this makes it possible to partially restore standard martingale convergence arguments that apply under correctly specified learning. Based on this, we derive general conditions to determine when beliefs in a given environment converge to some long-run belief either locally or globally (i.e. from some or all initial beliefs). We show that these conditions can be applied, first, to unify and generalize various convergence results in previously studied settings. Second, they enable us to analyse environments where learning is “slow”, such as costly information acquisition and sequential social learning. In such environments, we illustrate that even if agents learn the truth when they are correctly specified, vanishingly small amounts of misspecification can generate extreme failures of learning.
A NATIONAL SURVEY OF TRACEABILITY OF ACTIVITY METERS IN LITHUANIAN HOSPITALS
Authors: Skovorodko Kirill , Gudelis Arūnas 
Published: July 2022

Abstract
The activity of prescribed radiopharmaceuticals, which are administered for diagnostic and therapeutic purposes, strongly depends on the accuracy of the measuring equipment used in nuclear medicine. This study presents the current status of uncertainty measurements of activity meters used in Lithuanian hospitals. During 2016–2021, the Ionizing Radiation Metrology Laboratory of the Center for Physical Sciences and Technology, which is the National Metrology Institute, performed a comparison of activity meters in the nuclear medicine departments of Lithuanian hospitals. Responses of 16 activity meters that were used in the daily hospital practice were compared with the reference standard. In total, around 150 measurements of activity of diagnostic, therapeutic and calibration radionuclides in different sources and geometries were fulfilled. The results of the maximum deviation were determined to be 8.9% for calibration sources, 18.3% for diagnostic radionuclides and 20.1% for radionuclides used for therapeutic purposes.
Concluding Reflections from the former UNHRC Special Rapporteur on Violence Against Women, its Causes and Consequences (2009–15)
Authors: Manjoo Rashida 
Published: July 2022

Abstract
This concluding chapter provides an overview of the chapters, as well as briefly highlighting the relevant normative frameworks applicable to the issues addressed in this special edition journal. The authors have addressed structural, institutional, and individual gaps and challenges in the refugee protection sphere and have raised concerns about the lack of adequate acknowledgement of gendered aspects of the asylum frameworks and processes, and crucially the differential impact thereof. The gaps in the legally binding instruments governing this area of human rights protection, and the minimal attention to the connection between theory and practice and its resulting consequences, are highlighted by some authors.
The effects of varying levels of trace mineral supplementation on performance, carcass characteristics, mineral balance, and antibody concentrations in feedlot cattle
Authors: Lippy Brittany A , Robison Colton A , Wilson Blake K 
Published: July 2022

Abstract
The objective of this experiment was to determine the effects of increasing trace mineral (TM) supplementation on finishing cattle performance, carcass characteristics, TM balance, and antibody concentrations. Commercial Angus steers (n = 240; body weight, BW = 291 kg ± 27.4) were stratified by arrival BW and source and randomly assigned to 1 of 4 experimental treatments in a randomized complete block design (12 pens/treatment; 5 steers/pen). All steers underwent a TM depletion period for a minimum of 42-d prior to the administration experimental treatments. Treatments included a negative control (CON) in which cattle received no additional TM supplementation or TM supplementation treatments in which cattle received added Co, Cu, I, Mn, Se, or Zn from inorganic TM sources at 2016 Nutrient Requirements of Beef Cattle (NASEM) requirement levels (1X), at 2 times NASEM requirements (2X), or at 4 times NASEM requirements (4X). Selenium was included at 0.1, 0.2, and 0.3 mg/kg for 1X, 2X, and 4X respectively, based on federal law. There was no difference in overall BW, average daily gain (ADG), dry matter intake (DMI), or gain to feed (G:F) due to TM supplementation (CON vs. SUPP P ≥ 0.47). There was no difference in hot carcass weight, rib eye area, fat thickness, dressing percentage, marbling score, or USDA Yield Grade due to TM supplementation (CON vs. SUPP P ≥ 0.30). One steer was chosen at random from each pen to be evaluated for serum and liver TM status and antibody concentrations to common respiratory viruses. There was a treatment × day interaction for serum Co and liver Cu and Se (P &lt; 0.0001). Serum Co was greatest for the 4X treatment from d 28 through harvest. Liver Cu was greatest for the 2X and 4X treatments from d 56 through harvest. Liver Se was greatest for 2X and 4X from d 28 through harvest. Serum Zn was greatest for the 4X treatment (P = 0.02). There was an effect of day on liver Co, Fe, Mn, Mo, and Zn (P ≤ 0.0001) and serum Cu, Mn, Mo, Se, and Zn (P ≤ 0.002). Individual TM concentrations differed over time; however, none were ever considered deficient or toxic based on published reference ranges. There was an effect of time on bovine viral diarrhea virus Type 1A, bovine herpesvirus type 1, and bovine parainfluenza 3 virus antibody concentrations (P ≤ 0.0001). Supplementation of TM above NASEM requirements did not affect overall cattle performance, carcass characteristics, or antibody concentrations, but did affect the storage and circulation of certain TM.