Miracle-dz/UniFAR-FTUs huggingface dataset:
Solutrean hypothesis: genetics, the mammoth in the room

Abstract The Solutrean hypothesis for the origin of the Clovis archaeological culture contends that people came from south-western Europe to North America during the Last Glacial Maximum. This hypothesis has received numerous critiques, but little objective testing, either of cultural or genetic evidence. We contest the assertion that there is NO genetic evidence to support this hypothesis, and detail the published evidence, consistent with a pre-Columbian western Eurasian origin for some founding genetic markers, specifically mtDNA X2a, and some autosomal influence, found in ancient and modern Native American populations. The possibility that the inferred pre-Columbian western autosomal influence came more directly than through Siberia is not even considered in such studies. The mtDNA X2a evidence is more consistent with the Atlantic route and dates suggested by the Solutrean hypothesis and is more parsimonious than the assumption of a single Beringian entry, that assumes retrograde extinction of X in East Eurasia.
RNA sequencing identifies a cryptic exon caused by a deep intronic variant in NDUFB10 resulting in isolated Complex I deficiency.

The diagnosis of mitochondrial disorders remains a challenging and often unmet need. We sought to investigate a sibling pair with suspected mitochondrial disease and a clinical presentation notable for global developmental delay, poor growth, sensorineural hearing loss, and brain MRI abnormalities, both with early death. Following uninformative exome and genome sequencing of the family quartet, RNA sequencing was pursued as an orthogonal testing strategy. RNA sequencing of fibroblasts from the older sibling identified the presence of a cryptic exon in intron 1 of NDUFB10, that included an in-frame stop codon. NDUFB10 encodes a subunit of mitochondrial OXPHOS complex I. Differential expression analysis relative to control samples suggested significantly decreased expression. The cryptic exon was found to contain a rare intronic variant, NM_004548. 3:c.131-442G>C, that was homozygous in both affected siblings and absent from population allele frequency databases. Immunoblot and quantitative proteomic analysis of fibroblasts from the older sibling revealed decreased abundance of complex I subunits associated with NDUFB10, providing evidence of isolated complex I deficiency. Biallelic variants in NDUFB10 have previously been reported in a single individual with infantile-onset mitochondrial disease. We present data implicating a deep intronic variant in NDUFB10 as the cause of mitochondrial disease in two further individuals. This variant results in loss of expression and overall destabilization of mitochondrial OXPHOS complex I and highlights the importance of RNA sequencing as a complementary diagnostic tool in patients undergoing genome-wide diagnostic evaluation.
Massive-MIMO Configuration of Multipolarized ULA and UCA in 5G Wireless Communications

Massive-Multiple Input Multiple Output (M-MIMO) is a new technology offers large antenna at the Base Station (BS), simultaneously serving multiple single-antenna users. In this paper, two geometrical channels are established and compared, based on Plane Wave (PW) and Spherical Wave (SW). The Multipolarized-Uniform-Linear-Array Massive-MIMO (MULA-mMIMO) and Multipolarized-Uniform-Circular-Array Massive-MIMO (MUCA-mMIMO) systems are used to decrease the channel orthogonality. The three dimensional MUCA-mMIMO and MULA-mMIMO are evaluated and analyzed for various parameters. Simulation results demonstrate that MUCA-mMIMO performs better than MULA-mMIMO, and will be the best choice for the new technology Massive-MIMO.
Taxonomy and biogeography of the African Pygmy mice, Subgenus Nannomys (Rodentia, Murinae, Mus) in Ivory Coast and Guinea (West Africa)

Abstract Recent investigations in Guinea and Ivory Coast showed that Mus (Nannomys) are hosts of new arenaviruses. However, the taxonomy and biogeography of the western pygmy mice are poorly known, as this genus contains many cryptic species. To improve our taxonomic knowledge on this subgenus and its distribution range in West Africa, we performed a molecular, cytogenetical and morphological study of all Mus (Nannomys) species in this part of Africa. This approach allowed us to detect five species in Guinea (Mus mattheyi, M. minutoides, M. setulosus, M. baoulei, M. musculoides) and four (M. minutoides, M. setulosus, M. baoulei, M. musculoides) in Ivory Coast. Our molecular results confirm the validity of M. baoulei and the extended distribution range of M. mattheyi. We also observed a high degree of genetic differentiation between and within these species, especially within the M. setulosus clade which may be a species complex. The canonical analyses on the craniometrical and external morphological features of the sequenced specimens are insufficient to perfectly separate the studied species. Nevertheless, our results confirm that M. setulosus and M. baoulei are the largest Mus species that occur in Guinea and Ivory Coast. M. baoulei can be distinguished by its short tail and M. setulosus by an enlarged and bilobated lower molar (M3). Among the smaller species, M. musculoides is difficult to identify using morphological data alone, but differences in tail length proportions, size of tympanic bullae, the length and shape of the upper dental row allow identification of this species with some confidence. Our results allow us to provide some conclusions about the distribution ranges of the studied Mus (Nannomys) spp. in both countries and to discuss their presence in relation to vegetation, habitat and human settlements.
Association of age, sex, comorbidities, and clinical symptoms with the severity and mortality of COVID-19 cases: a meta-analysis with 85 studies and 67299 cases

Background: A new pathogenic disease named COVID-19 became a global threat, first reported in Wuhan, China, in December 2019. The number of affected cases growing exponentially and now, more than 210 countries confirmed the cases. Objective: This meta-analysis aims to evaluate risk factors, the prevalence of comorbidity, and clinical characteristics in COVID-19 death patients compared to survival patients that can be used as a reference for further research and clinical decisions. Methods: PubMed, Science Direct, SAGE were searched to collect data about demographic, clinical characteristics, and comorbidities of confirmed COVID-19 patients from January 1, 2020, to May 17, 2020. Meta-analysis was performed with the use of Review Manager 5.3 Results: Eighty-five studies were included in Meta-analysis, including a total number of 67,299 patients with SARS-CoV-2 infection. Males are severely affected or died than females (OR = 2.26, p < 0.00001; OR = 3.59, p < 0.00001) are severely affected, or died by COVID-19 and cases with age [≥]50 are at higher risk of death than age <50 years (OR=334.23). Presence of any comorbidity or comorbidities like hypertension, cardiovascular disease, diabetes, cerebrovascular disease, respiratory disease, kidney disease, liver disease, malignancy significantly increased the risk of death compared to survival (OR = 3.46, 3.16, 4.67, 2.45, 5.84, 2.68, 5.62, 2.81,2.16). Among the clinical characteristics such as fever, cough, myalgia, diarrhea, abdominal pain, dyspnea, fatigue, sputum production, chest tightness headache and nausea or vomiting, only fatigue (OR = 1.31, 95%) and dyspnea increased the death significantly (OR= 1.31, 4.57). The rate of death of COVID-19 cases is 0.03-times lower than the rate of survival (OR = 0.03). Conclusion Our result indicates that male patients are affected severely or died, the rate of death is more in the age [≥]50 group, and the rate of death is affected by comorbidities and clinical symptoms.
Das Experiment: Geißelregeneration bei Chlamydomonas reinhardii

Viele einzellige Organismen bewegen sich mit Hilfe einer oder mehrerer Geifleln fort, um ein fur sie optimales Milieu aufsuchen zu konnen, was den Bestand gewahrleistet. Ein klassisches Beispiel hierfur sind die Anioben, die sich bei Nahrungsmangel in Flagellaten und nach Auffinden giinstiger Nahrungsbedingungen wieder in Amoben umwandeln [I]. Der Aufbau einer eukaryotischen GeiRel ist in Abbildung 1 schematisch wiedergegeben. Gegeniiber der prokaryotischen unterscheidet sie sich sowohl ini Aufbau wie in physiologischen Eigenschaften. Das Interesse der Zellbiologen erweckte die eukaryotische Geiflel in den letzten beiden Dekaden nicht zuletzt wegen des gehauften Auftretens von Mikrotubuli, die in eineni charakteristischen Grundniuster angeordnet sind (siehe d a m auch BIUZ 13, Heft 6, 1983). Aus Abbildung 1 ist ersichtlich, daR neun Doppelmikrotubuli im peripheren Bereich in gleichen Abstanden voneinander einen Kreis bilden, dessen Mittelbereich von einem Mikrotubulipaar besetzt ist. Der zentrale Bereich niit den beiden Mikrotubuli ist durch sog. ,,Speichen" mit den Doppelmikrotubuli verbunden. Letztere besitzen an dem als A-Mikrotubulus bezeichneten Teil zwei Seitenarme, die insbesondere aus Proteinen bestehen, die zur Umsetzung des zellularen Energietragcrs (ATP) befahigt sind und den Namcn Dynein erhielten. Die Basalltorper, die kurz unterhalb der Plasmamembran liegen, dienen als Organisationszentrum fiir die peripharen Doppelmikrotubuli. Sie konnen als modifizierte Centriole angesehen werden.
The Performance of a Metaheuristic Algorithm for Finding a Maximal Weight Clique in the Fill-in-Blank Problem

A programming education is one of the most important fields in Information and Education Technology. Funabiki et al. have developed a Web-based Java Programming Learning Assistant System (JPLAS). JPLAS mainly provides two types of problems, namely the code writing problem and the fill-in-blank problem, to support students' self-studies at various learning levels. Particularly in the fill-in-blank problem (FIBP), the system requires an efficient algorithm to find a maximal clique of the compatibility graph in advance in order to obtain a maximal set of blank elements with unique answers. In this paper, we investigate the performance of a metaheuristic algorithm based on an iterated local search for solving the maximum weight clique problem (MWCP), which is an important generalization of the maximum clique problem, given as an extension of the compatibility graph in the FIBP. Computational results show that our metaheuristic algorithm is capable of finding satisfactory weighted cliques efficiently for well-known benchmark graphs and the performance of our algorithm is comparable to those of state-of-the-art metaheuristics for the MWCP.
Sphingosine 1‐phosphate induces EGFR expression via Akt/NF‐κB and ERK/AP‐1 pathways in rat vascular smooth muscle cells

Sphingosine 1‐phosphate (S1P) has been shown to regulate expression of several genes in vascular smooth muscle cells (VSMCs) and contributes to arteriosclerosis. However, the mechanisms regulating epidermal growth factor receptor (EGFR) expression by S1P in aortic VSMCs remain unclear. Western blotting and RT‐PCR analyses showed that S1P induced EGFR mRNA and protein expression in a time‐ and concentration‐dependent manner, which was attenuated by inhibitors of MEK1/2 (U0126) and phosphatidylinositide 3‐kinase (PI3K; wortmannin), and transfection with dominant negative mutants of ERK and Akt, respectively. These results suggested that S1P‐induced EGFR expression was mediated through p42/p44 MAPK and PI3K/Akt pathways in VSMCs. In accordance with these findings, S1P stimulated phosphorylation of p42/p44 MAPK and Akt which was attenuated by U0126 and wortmannin, respectively. Furthermore, S1P‐induced EGFR upregulation was blocked by a selective NF‐κB inhibitor helenalin. Immunofluorescent staining and reporter gene assay revealed that S1P‐induced activation of NF‐κB was blocked by wortmannin, but not by U0126, suggesting that activation of NF‐κB was mediated through PI3K/Akt. Moreover, S1P‐induced EGFR expression was inhibited by an AP‐1 inhibitor curcumin and tanshinone IIA. S1P‐stimulated AP‐1 subunits (c‐Jun and c‐Fos mRNA) expression was attenuated by U0126 and wortmannin, suggesting that MEK and PI3K/ERK cascade linking to AP‐1 was involved in EGFR expression. Upregulation of EGFR by S1P may exert a phenotype modulation of VSMCs. This hypothesis was supported by pretreatment with AG1478 or transfection with shRNA of EGFR that attenuated EGF‐stimulated proliferation of VSMCs pretreated with S1P, determined by XTT assay. These results demonstrated that in VSMCs, activation of Akt/NF‐κB and ERK/AP‐1 pathways independently regulated S1P‐induced EGFR expression in VSMCs. Understanding the mechanisms involved in S1P‐induced EGFR expression on VSMCs may provide potential therapeutic targets in the treatment of arteriosclerosis. J. Cell. Biochem. 103: 1732–1746, 2008. © 2007 Wiley‐Liss, Inc.
Design of TCP Congestion Control in Data Center Networks Based on Stable Round Trip Time

Data center networks have become increasingly important over the years as they are what make cloud computing, mobile computing, machine learning, and artificial intelligence possible. TCP is the main transport layer protocol in the Internet. Its congestion control has evolved for decades, with many versions or variants having been proposed and improved. Among them, several well-known TCP versions have been implemented either in different versions of the OS kernel or in the data center. Whether it is based on packet loss, round-trip-time (RTT), or bandwidth-delay product (BDP), each has its own advantages and disadvantages. In this paper, we will review the characteristics of the data center, and then propose a TCP version that is more suitable for the data center and achieves reliable transmission with high throughput and low latency.
A Learning Ability Evaluation Method Based On Item Response Theory and Machine Learning Method

In recent years, online education and MOOC (Massive Open Online Courses) education have arisen. This paper proposes a learner ability modeling method based on item response theory and machine learning method. We use item response theory to calculate intermediate parameters and use machine learning to predict learners' learning ability after learning a new course. At the same time, this paper also presents a solution to the cold start problem. Compared to the traditional machine learning prediction method, the models of this paper have certain advantages for the learning ability prediction method.
Just-in-time Parsing with Scannerless Earley Virtual Machines

Scannerless Earley Virtual Machines (SEVM) is a new generalized context-free parsing method, in which grammars are internally encoded using a special instruction intermediate language. In this paper we show how just-in-time compilation can be used to translate intermediate form grammars into native machine code to achieve improved parsing performance. We also present an efficient method for lexical disambiguation, which additionally enables to significantly reduce the amount of code that needs to be just-in-time compiled. Finally, we compare our implementation of SEVM with other parser implementations and show that our parser provides acceptable performance for analysing real-world computer languages.
Report on the Emergence Time of a Species of Thitarodes Ghost Moth (Lepidoptera: Hepialidae), Host of the Caterpillar Fungus Ophiocordyceps sinensis (Ascomycota: Ophiocordycipitaceae) in Uttarakhand, India

Abstract Ghost moths in the genus Thitarodes Viette, 1968, are hosts of the economically important caterpillar fungus, which is harvested in high mountain meadows across the Hengduan mountains and the Himalayas. In northwestern India, although caterpillar fungus has been collected in the state of Uttarakhand, no adults of Thitarodes species have been recorded. We report the sighting of a female pupa of Thitarodes sp. and its last-instar molt at Munsiyari, Uttarakhand, India, on 5 July 2019 and estimate that the adult emergence time in this habitat should be late July or early August. Although the habitats of caterpillar fungus in Uttarakhand are geographically closer to those in Nepal, they are climatically more similar to habitats of caterpillar fungus in Qinghai province in China. Among records at the same elevation, climatic variables are highly predictive of the emergence date of Thitarodes adults (adjusted-R2: 0.7925, F = 6.27, P = 0.03). Our result highlights the role of the Himalayan mountains as both a north–south climatic barrier and an east–west climatic gradient. We encourage local stakeholders and scientists in Uttarakhand to survey adult emergences of Thitarodes from July to mid-August.
Medical Application of Calcium Orthophosphate Bioceramics

In the late 1960’s, a strong interest was raised in biomedical applications of ceramic materials (named bioceramics a little bit later). Bioceramics was initially used as reasonable alternatives to metals in order to increase their biocompatibility. However, within a short period, it has grown into a diverse class of biomaterials, presently including three essential types: relatively bioinert, bioactive (or surface reactive) and bioresorbable bioceramics. This review is limited to bioceramics prepared from calcium orthophosphates only, which belong to the categories of bioactive and bioresorbable compounds. There have been a number of important advances in this field during the past 30 – 40 years. The research was shifted from an initial study on the develop-ment of bioinert bioceramics towards bioactive and bioresorbable bioceramics, and these different types of calcium orthophosphate bioceramics can be tuned through the structural and compositional control. At the turn of the millennium, a new concept of calcium orthophosphate bioceramics has been developed to promote a regeneration of bones. Current biomedical applications of calcium orthophosphate bioceramics include artificial replacements for hips, knees, teeth, tendons and ligaments, as well as repair for periodontal disease, maxillofacial reconstruction, augmenttation and stabilization of the jawbone, spinal fusion and bone fillers after tumor surgery. Potential future applications of calcium orthophosphate bioceramics are demonstrated in drug delivery systems, effective carriers of growth factors, bioactive peptides and/or various types of cells for tissue engineering purposes.
Barriers and motivators to pre-exposure prophylaxis uptake among Black and Latina transgender women in Los Angeles: perspectives of current PrEP users

ABSTRACT The purpose of this qualitative study was to identify barriers and motivators to PrEP uptake from the perspective of Black and Latina transgender women (TW) who are currently using PrEP to suggest intervention and outreach activities to increase PrEP uptake in this population. The Information-Motivation-Behavioral Skills Model guided the development of the semi-structured interview guide. A thematic analysis approach was used to analyze the data. Perceived barriers to PrEP uptake included structural and logistic barriers, language and cultural barriers to medical engagement, lack of transgender competent or gender-affirming care, and prioritizing hormone therapy over the use of PrEP. To increase PrEP uptake among BLTW, participants recommended disseminating PrEP information through a variety of methods, highlighting relationship and sexual health benefits of using PrEP, and developing effective patient-provider communication. Our findings highlight several ways to promote PrEP among BLTW. PrEP promotion should be integrated into gender-affirming care and supported by peer education and navigation services that reach BLTW in both clinic and community settings.
Conducting eating disorders research in the time of COVID‐19: A survey of researchers in the field

Abstract The COVID‐19 pandemic has impacted research around the globe and required shuttering of research programs and the implementation of procedural adjustments to ensure safety. This study sought to document COVID‐19's impact on eating disorders (ED) research, which may be particularly susceptible to such disruptions, given its focus on individuals who are physically and emotionally vulnerable. We invited ED researchers from editorial boards and scientific organizations to complete a quantitative/qualitative survey about: COVID‐19's current and future impact on ED research; areas of concern about research disruptions; and effective strategies for conducting and supporting research during and after COVID‐19. Among 187 participants, many had moved studies online and/or shutdown part of their research. Across position types (permanent, 52.7%; temporary, 47.3%), participants reported high concern about data collection, recruitment, and securing future funding. Those holding temporary positions reported significantly greater concern about COVID‐19's impact on their career and greater stress than participants in permanent positions. Strategies for dealing with research disruptions included: employing technology; reprioritizing goals/tasks; and encouraging collaboration. Results underscore the high levels of stress and disruption caused by COVID‐19. We echo calls by our respondents for support for early career scholars and advocacy for additional resources for research and scientists.
Immunoglobulin interface redesigning to enhance lebrikizumab mediated immunomodulation of IL-13 hyper-response

Abstract The overexpression of interleukin-13 (IL-13) leads to autoimmune and inflammatory diseases. These adverse responses can be neutralized by using lebrikizumab as a therapeutic monoclonal antibody (mAb). Herein, we have attempted to modulate the lebrikizumab mAb to enhance its binding affinity towards IL-13. The interface residues of the lebrikizumab-IL-13 complex were determined by the PyMOL and verified by the artificial neural network-based B-cell epitope prediction server (ABCpred server) and the Paratome web server. The Cologne University Protein Stability Analysis Tool (CUPSAT) web server based mutational approach was used to identify the stable and favorable interface mutations in the lebrikizumab. Only 40 mutations were selected to generate a single mutant library, and their binding affinity for IL-13 was analyzed by using the Z-Dock server. Based on high Z-score, mutants having a better affinity with IL-13 were selected to create a multi-mutant library. The multi-mutant library was again subjected to the Z-Dock server, and their binding affinity was determined. The highest-scoring ten mAb mutants were validated by using PatchDock and ClusPro servers. The best two potential mAb mutants were identified and subjected to molecular dynamics (MD) simulations to ensure its structural stability at the microscopic level. The changes in the different bonds as the effect of mutation were assessed by LigPlot + v2.1. The AllerTOP and ToxinPred web servers were used to analyze the non-allergic and nontoxic nature of the selected mutants. Therefore, these redesigned mAb could be used for potential treatment against IL-13 associated diseased conditions. Communicated by Ramaswamy H. Sarma