Miracle-dz/UniFAR-FTUs huggingface dataset:
Ancient hybridization patterns between bighorn and thinhorn sheep

Whole‐genome sequencing has advanced the study of species evolution, including the detection of genealogical discordant events such as ancient hybridization and incomplete lineage sorting (ILS). The evolutionary history of bighorn (Ovis canadensis) and thinhorn (Ovis dalli) sheep present an ideal system to investigate evolutionary discordance due to their recent and rapid radiation and putative secondary contact between bighorn and thinhorn sheep subspecies, specifically the dark pelage Stone sheep (O. dalli stonei) and predominately white Dall sheep (O. dalli dalli), during the last ice age. Here, we used multiple genomes of bighorn and thinhorn sheep, together with snow (O. nivicola) and the domestic sheep (O. aries) as outgroups, to assess their phylogenomic history, potential introgression patterns and their adaptive consequences. Among the Pachyceriforms (snow, bighorn and thinhorn sheep) a consistent monophyletic species tree was retrieved; however, many genealogical discordance patterns were observed. Alternative phylogenies frequently placed Stone and bighorn as sister clades. This relationship occurred more often and was less divergent than that between Dall and bighorn. We also observed many blocks containing introgression signal between Stone and bighorn genomes in which coat colour genes were present. Introgression signals observed between Dall and bighorn were more random and less frequent, and therefore probably due to ILS or intermediary secondary contact. These results strongly suggest that Stone sheep originated from a complex series of events, characterized by multiple, ancient periods of secondary contact with bighorn sheep.
ERGONOMIC COMPLIANCE: A PILOT STUDY OF ONE FACULTY AT A ZIMBABWEAN ACADEMIC INSTITUTION

Work-related injuries and diseases are a major cause of concern worldwide. Despite the emergence of information technology and sedentary office work in third world countries like Zimbabwe, there is paucity of literature pertaining to ergonomic compliance. Certain ergonomic principles if adhered to can prevent work related musculoskeletal problems. We sought to analyse the level of compliance to workspace design ergonomic principles at one faculty of a Zimbabwean academic institution. We analysed the compliance to ergonomic principles among a cross section of randomly selected offices in 2011. The analysis covered information technology hardware, furniture and potential sources of stress using a questionnaire and checklist adapted from Marmaras and Papadopoulos (2003). Data were analysed descriptively. Participants were 36 employees, mostly female (83%) who held secretarial positions (58%). Most compliant aspects of the workstations were information technology hardware (80.5%) and the least compliant was furniture (45%). Information technology hardware and work environment were ergonomically friendly but positioning of the devices was not. There is need to upgrade the furniture as it had numerous shortcomings leading the workers to assume non- ergonomically friendly postures.
Dispersal of southern elephant seals (Mirounga leonina) from Davis Base, Antarctica: Combining population genetics and tracking data

Marine animals such as the southern elephant seal (Mirounga leonina) rely on a productive marine environment and are vulnerable to oceanic changes that can affect their reproduction and survival rates. Davis Base, Antarctica, acts as a moulting site for southern elephant seals that forage in Prydz Bay, but the genetic diversity and natal source populations of these seals has not been characterized. Determining the genetic diversity of moulting populations like this one provides essential information on seal dispersal, inter-population mixing, and foraging behaviours. In this study, we combined genetic and animal tracking data on these moulting seals to identify levels of genetic diversity, natal source population, and movement behaviours during foraging and haul-out periods. Using mitochondrial sequence data, we identified two major breeding lineages of seals at Davis Base. We found that the majority of the seals originated from breeding stocks within the South Atlantic Ocean and South Indian Ocean. One seal was grouped with the Macquarie Island breeding stock (South Pacific Ocean). The Macquarie Island population, unlike the other two stocks, is decreasing in size. Tracking data revealed long-distance foraging activity of the Macquarie Island seal around Crozet Islands. We speculate that changes to the Antarctic marine environment have resulted in a shift in foraging and dispersal strategies, which subsequently affects seal population growth rates. These findings have implications for conservation management plans aimed at improving the population status of the southern elephant seal.
Ionotropic glutamate receptors in the retina – a bioinformatical meta-analysis

Glutamate is an essential neurotransmitter for signal processing in the vertical pathway of the mammalian retina, where it is involved in the distribution of visual information into several parallel channels. The excitatory effects of glutamate are mediated by AMPA-, kainate-, and NMDA-type ionotropic glutamate receptors (iGluRs). The expression patterns of these receptors in the vertebrate retina have been investigated so far with mainly immunocytochemical, in-situ hybridization, and electrophysiological/pharmacological techniques. Here, we have used scRNA sequencing data from chicken, mouse, macaque, and human retina to describe and compare the profile of iGluR expression in major retinal cell types across species. Our results suggest that major retinal cell types each express a unique set of iGluRs with substantial differences between non-mammalian and mammalian retinae. Expression of iGluRs has been investigated in more detail for amacrine and bipolar cell types of the human retina, each showing minor variations of a common pattern. The differential expression of iGluRs is likely to convey unique signal processing properties to individual elements of the retinal circuitry.
Single-cell generalized trend model (scGTM): a flexible and interpretable model of gene expression trend along cell pseudotime

Motivation Modeling single-cell gene expression trends along cell pseudotime is a crucial analysis for exploring biological processes. Most existing methods rely on nonparametric regression models for their flexibility; however, nonparametric models often provide trends too complex to interpret. Other existing methods use interpretable but restrictive models. Since model interpretability and flexibility are both indispensable for understanding biological processes, the single-cell field needs a model that improves the interpretability and largely maintains the flexibility of nonparametric regression models. Results Here we propose the single-cell generalized trend model (scGTM) for capturing a gene’s expression trend, which may be monotone, hill-shaped, or valley-shaped, along cell pseudotime. The scGTM has three advantages: (1) it can capture non-monotonic trends that are still easy to interpret, (2) its parameters are biologically interpretable and trend informative, and (3) it can flexibly accommodate common distributions for modeling gene expression counts. To tackle the complex optimization problems, we use the particle swarm optimization algorithm to find the constrained maximum likelihood estimates for the scGTM parameters. As an application, we analyze several single-cell gene expression data sets using the scGTM and show that it can capture interpretable gene expression trends along cell pseudotime and reveal molecular insights underlying the biological processes. Availability and implementation The Python package scGTM is open-access and available at https://github.com/ElvisCuiHan/scGTM. Contact jli@stat.ucla. edu
Genome assembly of Danaus chrysippus and comparison with the Monarch Danaus plexippus

Milkweed butterflies in the genus Danaus are studied in a diverse range of research fields including the neurobiology of migration, biochemistry of plant detoxification, host-parasite interactions, evolution of sex chromosomes, and speciation. We have assembled a nearly chromosomal genome for Danaus chrysippus (known as the African Monarch, African Queen, and Plain Tiger) using long read sequencing data. This species is of particular interest for the study of genome structural change and its consequences for evolution. Comparison with the genome of the North American Monarch Danaus plexippus reveals generally strong synteny, but highlights three inversion differences. The three chromosomes involved were previously found to carry peaks of intra-specific differentiation in D. chrysippus in Africa, suggesting that these inversions may be polymorphic and associated with local adaptation. The D. chrysippus genome is over 40% larger than that of D. plexippus, and nearly all of the additional ∼100 Megabases of DNA comprises repeats. Future comparative genomic studies within this genus will shed light on the evolution of genome architecture.
Chloroplast transit peptides often require downstream unstructured sequence in Chlamydomonas reinhardtii

The N-terminal sequence stretch that defines subcellular targeting for most nuclear encoded chloroplast proteins is usually considered identical to the sequence that is cleaved upon import. Yet here this study shows that for nine out of ten tested Chlamydomonas chloroplast transit peptides, additional sequence past the cleavage site is required to enable chloroplast targeting. Using replacements of native post-cleavage residues with alternative sequences points to a role for unstructured sequence at mature protein N-termini.
Global engineering teams – a programme promoting teamwork in engineering design and manufacturing

Engineering graduates are expected to possess various competencies categorised into hard and soft skills. The hard skills are acquired through specific coursework, but the soft skills are often treated perfunctorily. Global Engineering Teams (GET) is a programme that promotes project-oriented tasks in virtual student teams working in collaboration with industry partners. Teamwork is a major success factor for GET as students always work in groups of varying sizes. A questionnaire-based survey of the 2008 cohort of GET students was conducted to assess teamwork, communication and conflict resolution among group members. The results confirmed that deliverables are readily achieved in teams and communication was open. A challenge of using virtual teams is the availability of high-speed Internet access. The GET programme shows that it is possible to deliver engineering design and manufacturing via industry/university collaboration. The programme also facilitates multidisciplinary teamwork at an international level.
Time course of EEG power during creative problem‐solving with insight or remote thinking

Problem-solving often requires creativity and is critical in everyday life. However, the neurocognitive mechanisms underlying creative problem-solving remain poorly understood. Two mechanisms have been highlighted: forming new connections from and between the problem elements and insight solving (with a sudden realization of a solution). We examined EEG activity during an adapted version of a classical insight problem task, the Remote Associates Test, that requires finding a word connecting three words. It allowed us to explore remoteness in semantic connections (by varying the remoteness of the solution word across trials) and insight solving (identified as a “Eurêka” moment reported by the participants). Semantic remoteness was associated with a power increase in alpha band (8-12Hz) in a left parieto-temporal cluster, beta band (13-30Hz) in a right fronto-temporal cluster in the early phase of the task, and theta band (3-7Hz) in frontal cluster before the participants responded. Insight solving was associated with power increase preceding the response in alpha and gamma band (31-60Hz) in left temporal clusters and theta band in a frontal cluster. Source reconstructions show the brain regions associated with these clusters. Overall, our findings shed new light on the dynamic of some of the mechanisms involved in creative problem-solving.
SHEAR STRENGTH OF REINFORCED AND PRESTRESSED CONCRETE DEEP BEAMS. PART II: THE SUPPORTING EVIDENCE.

Experimental data on prestressed concrete deep beams are still very scarce. To the authors' knowledge, the experimental programme described in this paper represents the first detailed programme to consider various tendon profiles and different degrees of prestressing. A total of 34 deep beams were tested, of which 13 beams were reinforced while the other 21 beams were prestressed. The results show that both the shear strength and the serviceability performance of deep beams are significantly improved by the use of prestressing and by the use of orthogonal web reinforcement. The following factors were also investigated: deep beam deformation, ultimate behaviour, various cracking loads, modes of failures, main tension steel, various types of web reinforcements, strains in reinforcements and span-to-depth ratio. In addition to clarifying various factors affecting the behaviour of concrete deep beams, this paper provides a comprehensive supporting evidence for the authors' proposed equation described in a companion paper (Part I) (IRRD 898903).
Couching the brain’s multiple-demand and language-specific systems within a macroscale gradient of cortical connectivity

The cerebrum comprises a set of specialised systems that tile across the cortical sheet, forming a tapestry-like configuration. For example, the multiple-demand and language-specific systems occupy largely separate neural estates and exhibit disparate functional profiles. Although delimiting the boundary between systems informs where cortical sheet functionally fractionates, it remains unclear why different systems’ topographical placements are spatially configured in typical manners and how a macroscale architecture arises from this topography. Novel approaches have tackled this challenge by condensing the topography into a principal gradient, which represents the workflow of information processing from sensory-motoric to abstract-cognitive. To understand how the multiple-demand and language-specific systems are accommodated in the gradient framework, here we used fMRI to probe cognitive operations in semantic vs. visuospatial domains and projected functional activities onto the principal gradient. We found that the two systems showed distinct trajectories of distribution along gradient tiers, suggesting different roles in the transition from sensation to cognition. Critically, when semantic processing became difficult, the brain recruited a specialised ‘semantic-control’ system that was a functional and anatomical ‘hybrid’ juxtaposed between the multi-demand and language systems. We discuss how the brain’s modular division can be better understood through the lens of a dimensionality-reduced gradient-like architecture.
Human-in-the-Loop Systems for Truthfulness: A Study of Human and Machine Confidence

Automatically detecting online misinformation at scale is a challenging and interdisciplinary problem. Deciding what is to be considered truthful information is sometimes controversial and difﬁcult also for educated experts. As the scale of the problem increases, human-in-the-loop approaches to truthfulness that combine both the scalability of machine learning (ML) and the accuracy of human contributions have been considered. In this work we look at the potential to automatically combine machine-based systems with human-based systems. The former exploit supervised ML approaches; the latter involve either crowd workers (i.e., human non-experts) or human experts. Since both ML and crowdsourcing approaches can produce a score indicating the level of conﬁdence on their truthfulness judgments (either algorithmic or self-reported, respectively), we address the question of whether it is feasible to make use of such conﬁdence scores to effectively and efﬁciently combine three approaches: (i) machine-based methods; (ii) crowd workers, and (iii) human experts. The three approaches differ signiﬁcantly as they range from available, cheap, fast, scalable, but less accurate to scarce, expensive, slow, not scalable, but highly accurate.
The Effects of Sporting and Physical Practice on Visual and Kinesthetic Motor Imagery Vividness: A Comparative Study Between Athletic, Physically Active, and Exempted Adolescents

The interest of motor imagery practice on performance and motor learning is well-established. However, the impact of sporting and physical practice on motor imagery vividness is currently unclear, especially in youth. Two-hundred-and-forty adolescents were recruited to form different groups. For each age group (age-group 1, A-G1 with 13years≤age≤14years 6months vs. age-group 2, A-G2 with 14years 6months<age≤16years), 40 athletes, 40 active adolescents, and 40 exempted were recruited (20 girls and 20 boys in each category). Movement Imagery Questionnaire-Revised Second version (MIQ-Rs) was used to assess the Visual Motor Imagery (VMI) and Kinesthetic Motor Imagery (KMI) vividness. Results show that VMI is more evoked and more vivid than KMI (p<0.001). Athletes had greater VMI and KMI than active and exempted groups (p<0.001), and the active group also performed higher VMI and KMI than the exempted group (p<0.001). Subjects from A-G2 had greater motor imagery than subjects from A-G1, and boys had better motor imagery than girls. Conclusion: the present results show that sport and physical education engagement is associated with enhanced motor imagery vividness, especially in VMI. Moreover, older adolescents evoke clearer images than younger adolescents, and boys have greater imagery ability than girls. Therefore, teachers and coaches should consider age and gender when developing this cognitive skill when learning, in physical education classes and sports clubs.
Defining the Spectrum, Treatment and Outcome of Patients With Genetically Confirmed Gorlin Syndrome From the HIT-MED Cohort

Gorlin syndrome is a genetic condition associated with the occurrence of SHH activated medulloblastoma, basal cell carcinoma, macrocephaly and other congenital anomalies. It is caused by heterozygous pathogenic variants in PTCH1 or SUFU. In this study we included 16 patients from the HIT2000, HIT2000interim, I-HIT-MED, observation registry and older registries such as HIT-SKK87, HIT-SKK92 (1987 – 2020) with genetically confirmed Gorlin syndrome, harboring 10 PTCH1 and 6 SUFU mutations. Nine patients presented with desmoplastic medulloblastomas (DMB), 6 with medulloblastomas with extensive nodularity (MBEN) and one patient with classic medulloblastoma (CMB); all tumors affected the cerebellum, vermis or the fourth ventricle. SHH activation was present in all investigated tumors (14/16); DNA methylation analysis (when available) classified 3 tumors as iSHH-I and 4 tumors as iSHH-II. Age at diagnosis ranged from 0.65 to 3.41 years. All but one patient received chemotherapy according to the HIT-SKK protocol. Ten patients were in complete remission after completion of primary therapy; four subsequently presented with PD. No patient received radiotherapy during initial treatment. Five patients acquired additional neoplasms, namely basal cell carcinomas, odontogenic tumors, ovarian fibromas and meningioma. Developmental delay was documented in 5/16 patients. Overall survival (OS) and progression-free survival (PFS) between patients with PTCH1 or SUFU mutations did not differ statistically (10y-OS 90% vs. 100%, p=0.414; 5y-PFS 88.9% ± 10.5% vs. 41.7% ± 22.2%, p=0.139). Comparing the Gorlin patients to all young, SHH activated MBs in the registries (10y-OS 93.3% ± 6.4% vs. 92.5% ± 3.3%, p=0.738; 10y-PFS 64.9%+-16.7% vs. 83.8%+-4.5%, p=0.228) as well as comparing Gorlin M0 SKK-treated patients to all young, SHH activated, M0, SKK-treated MBs in the HIT-MED database did not reveal significantly different clinical outcomes (10y-OS 88.9% ± 10.5% vs. 88% ± 4%, p=0.812; 5y-PFS 87.5% ± 11.7% vs. 77.7% ± 5.1%, p=0.746). Gorlin syndrome should be considered in young children with SHH activated medulloblastoma, especially DMB and MBEN but cannot be ruled out for CMB. Survival did not differ to patients with SHH-activated medulloblastoma with unknown germline status or between PTCH1 and SUFU mutated patients. Additional neoplasms, especially basal cell carcinomas, need to be expected and screened for. Genetic counselling should be provided for families with young medulloblastoma patients with SHH activation.
Emerging School Readiness Profiles: Motor Skills Matter for Cognitive- and Non-cognitive First Grade School Outcomes

A promising approach for studying school readiness involves a person-centered approach, aimed at exploring how functioning in diverse developmental domains conjointly affects children’s school outcomes. Currently, however, a systematic understanding lacks of how motor skills, in conjunction with other school readiness skills, affect a child’s school outcomes. Additionally, little is known about longitudinal associations of school readiness with non-academic (e.g., socioemotional) school outcomes. Therefore, we examined the school readiness skills of a sample of Dutch children (N = 91) with a mean age of 3 years and 4 months (46% girls). We used a multi-informant test battery to assess children’s school readiness in terms of executive functions (EFs), language and emergent literacy, motor skills, and socioemotional behavior. During the spring term of a child’s first grade year, we collected academic and non-academic (i.e., EFs, motor skills, socioemotional- and classroom behavior, and creative thinking) school outcomes. A latent profile analysis revealed four distinct profiles. Children in the “Parent Positive” (29%) profile were rated positively by their parents, and performed variably on motor and language/emergent literacy skills tests. The second profile–“Multiple Strengths” (13%)–consisted of children showing strengths in multiple domains, especially with respect to motor skills. Children from the third profile–“Average Performers” (50%)–did not show any distinct strengths or weaknesses, rather displayed school readiness skill levels close to, or just below the sample mean. Finally, the “Parental Concern” (8%) profile was characterized by high levels of parental concerns, while displaying slightly above average performance on specific motor and language skills. Motor skills clearly distinguished between profiles, next to parent-rated EFs and socioemotional behavior, and to a lesser extent emergent literacy skills. School readiness profiles were found to differ in mean scores on first grade academic achievement, parent- and teacher-rated EFs, motor skills, parent-rated socioemotional functioning, and pre-requisite learning skills. The pattern of mean differences was complex, suggesting that profiles could not be ranked from low to high in terms of school outcomes. Longitudinal studies are needed to disentangle the interaction between emerging school readiness of the child and the surrounding context.