Miracle-dz/UniFAR-FTUs huggingface dataset:
The Neogene Savannas of North America: A Retrospective Analysis on Artiodactyl Faunas

Savanna-like ecosystems were present at high latitudes in North America during much of the Neogene. Present-day African savannas, like the Serengeti, have been proposed to be modern analogs of these paleosavannas, particularly those from the middle Miocene of the Great Plains region of the United States. Both these extant and extinct savannas contain a preponderance of artiodactyl (even-toed ungulate) species; however, the taxonomic composition of each fauna is different. While present-day African savannas are dominated by ruminants (primarily bovids), the Neogene savannas of North America were dominated by a diversity of both camelid and non-bovid ruminant families. This study provides a quantitative test of the similarity of the artiodactyl faunas of the North American Neogene paleosavannas to those of the modern-day African savannas. A correspondence analysis of ecomorphological features revealed considerable overlap between modern and fossil faunas. The morphospace occupation of the extinct North American ruminants falls within that of the African bovids. Some of the extinct camelids also fall within this same morphospace, but many do not, perhaps indicating an environmental difference such as greater aridity in Neogene North America. The diversity and disparity of artiodactyl faunas through the Neogene of North America changed along with changing temperatures and precipitation regimes. The taxonomic and ecomorphological diversity of the Serengeti ruminant fauna is statistically comparable to those North American paleofaunas occurring during or immediately after the Middle Miocene Climatic Optimum (MMCO), but the later, more depauperate faunas are no longer comparable. This study quantitatively analyzes artiodactyl communities as they changed with the cooling and drying trend seen during the Neogene.
PHY-IDS: a physical-layer spoofing attack detection system for wearable devices

In modern connected healthcare applications, wearable devices supporting real-time monitoring and diagnosis have become mainstream. However, wearable systems are exposed to massive cyberattacks that threaten not only data security but also human safety and life. One of the fundamental security threats is device impersonation. We therefore propose PHY-IDS; a lightweight real-time detection system that captures spoofing attacks leveraging on body motions. Our system utilizes time series of physical layer features and builds on the fact that it is non-trivial to inject malicious frames that are indistinguishable with legitimate ones. With the help of statistical learning, our system characterizes the signal behavior and flags deviations as anomalies. We experimentally evaluate PHY-IDS's performance using bodyworn devices in real attack scenarios. For four types of attackers with increasing knowledge of the deployed detection system, the results show that PHY-IDS detects naive attackers with high accuracy above 99.8\% and maintains good accuracy for stronger attackers at a range from 81.0% to 98.9%.
Hypothermia-Induced Ubiquitination of Voltage-Dependent Anion Channel 3 Protects BV2 Microglia Cells From Cytotoxicity Following Oxygen-Glucose Deprivation/Recovery

Background: Hypothermia attenuates microglial activation and exerts a potential neuroprotective effect against cerebral ischemic-reperfusion (I/R) injury. However, the underlying mechanism remains to be elucidated. In this in vitro study, a model of oxygen-glucose deprivation, followed by recovery (OGD/R), was used to investigate whether hypothermia exerts anti-inflammatory and anti-apoptosis properties via enhanced ubiquitination and down-regulation of voltage-dependent anion channel 3 (VDAC3) expression. Methods: BV2 microglia were cultured under OGD for 4 h following reperfusion with or without hypothermia for 2, 4, or 8 h. M1 and M2 microglia markers [inducible nitric oxide synthase (iNOS) and arginase (Arg)1] were detected using immunofluorescence. The levels of pro-inflammatory cytokines [tumor necrosis factor (TNF) α, interleukin (IL)-1β], and anti-inflammatory factor (IL-10) were determined using enzyme-linked immunosorbent assay (ELISA). Mitochondrial membrane potential (ΔΨm) was assayed by JC-1 staining using a flow cytometer. Expression of caspase-3, cleaved caspase-3, and VDAC3 were assessed using western blot analysis. The cellular locations and interactions of ubiquitin and VDAC3 were identified using double immunofluorescence staining and immunoprecipitation (IP) assay. Also, the level of the VDAC3 mRNA was determined using a quantitative polymerase chain reaction (qPCR). Results: Hypothermia inhibited the OGD/R–induced microglia activation and differentiation into the M1 type with pro-inflammatory effect, whereas it promoted differentiation to the M2 type with anti-inflammatory effect. Hypothermia attenuated OGD/R-induced loss of Δψm, as well as the expression of apoptosis-associated proteins. Compared to normothermia, hypothermia increased the level of ubiquitinated VDAC3 in the BV2 microglia at both 2 and 8 h of reperfusion. Furthermore, hypothermia did not attenuate VDAC3 mRNA expression in OGD/R-induced microglia. Conclusions: Hypothermia treatment during reperfusion, attenuated OGD/R-induced inflammation, and apoptosis in BV2 microglia. This might be due to the promotion of VDAC3 ubiquitination, identifying VDAC3 as a new target of hypothermia.
An Efficient and Footprint-Free Protocol for the Transdifferentiation of Hepatocytes Into Insulin-Producing Cells With IVT mRNAs

Background Direct transdifferentiation of adult somatic cells into insulin-producing cells (IPCs) is a promising approach for cell-based therapies for type 1 diabetes mellitus. Liver cells are an ideal source for generating IPCs because they have regenerative ability and a developmental process similar to that of the pancreas. Pancreas versus liver fate is regulated by TALE homeoprotein (TGIF2) during development. Here, we wanted to investigate whether TGIF2 could enhance the efficiency of transdifferentiation of hepatocytes into IPCs induced by three pancreatic transcription factors (pTFs), i.e., Pdx1, NeuroD, and Mafa, which are crucial for pancreatic development in the embryo. Methods The in vitro transcribed (IVT) mRNAs of TGIF2 and the three pTFs were synthesized in vitro and sequentially supplemented in hepatocytes. On day 6, the expression of transcription factors was assessed by quantitative real-time polymerase chain reaction (qRT-PCR), and insulin expression was detected by immunofluorescence. Glucose-stimulated insulin secretion was assessed by enzyme-linked immunosorbent assay (ELISA). The key genes controlling cell polarity and the Wnt/PCP signaling pathway were assayed by qRT-PCR, and the level of JNK protein phosphorylation, which regulates the Wnt/PCP signaling pathway, was detected by western blotting. Results IVT mRNAs could be efficiently transfected into hepatocytes. Quantitative real-time polymerase chain reaction results revealed that compared with ectopic expression of the three pTFs alone, ectopic expression of the three pTFs plus TGIF2 could strongly reduce hepatic gene expression and subsequently improve the induction of a set of pancreatic genes. Immunofluorescence analysis showed that TGIF2 expression could double the transdifferentiation yield; 30% of the cells were insulin positive if induced by TGIF2 plus the 3 pTFs, while only 15% of the cells were insulin positive if induced by the three pTFs alone. ELISA analysis confirmed that glucose-stimulated insulin secretion was less efficient after transfection with the three pTFs alone. The differentiated cells derived from the addition of TGIF2 mRNA could form islet-like clusters. By contrast, the cells differentiated with the three pTFs did not form clusters under the same conditions. Tgif2 induced transdifferentiation more efficiently by remodeling the expression of genes in the Wnt/PCP pathway. Overexpression of TGIF2 in hepatocytes could activate the expression of key genes controlling cell polarity and genes in the Wnt/PCP signaling pathway, increasing the level of JNK protein phosphorylation. Conclusions Our study established a novel footprint-free protocol for efficient transdifferentiation of hepatocytes into IPCs using IVT mRNAs of TGIF2 and 3 pTFs, which paved the way toward a clinical application.
Chapter 5: Subspecies are for Convenience

Abstract The century-long debate over the meaning and utility of the subspecies concept has produced spirited print but only superficial consensus. I suggest that genuine consensus about subspecies is an impossible goal, because trinomial epithets will inevitably be applied to a heterogeneous mix of evolutionary phenomena, thereby precluding genuine standardization of the concept. Populations that have intermediate levels of phenotypic differentiation and geographic isolation from one another often fall into a region I refer to as the "zone of art," where even skilled experts can disagree about the validity of any one subspecific treatment. The trinomial system cannot accurately represent the kind of information now available about genetic and character variation across space. Instead, ever more accurate tools are being perfected for quantitative, standardized descriptions of variation. These analyses—not subspecies classifications—will keep providing new scientific insights into geographic variation. Eve.
Temporal evolution and adaptation of SARS-COV-2 codon usage

The outbreak of severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) has caused an unprecedented pandemic. Since the first sequenced whole-genome of SARS-CoV-2 on January 2020, the identification of its genetic variants has become crucial in tracking and evaluating their spread across the globe. In this study, we compared 134,905 SARS-CoV-2 genomes isolated from all affected countries since the outbreak of this novel coronavirus with the first sequenced genome in Wuhan, China to quantify the evolutionary divergence of SARS-CoV-2. Thus, we compared the codon usage patterns of SARS-CoV-2 genes encoding the membrane protein (M), envelope (E), spike surface glycoprotein (S), nucleoprotein (N), RNA-dependent RNA polymerase (RdRp). The polyproteins ORF1a and ORF1b were examined separately. We found that SARS-CoV-2 tends to diverge over time by accumulating mutations on its genome and, specifically, on the sequences encoding proteins N and S. Interestingly, different patterns of codon usage were observed among these genes. Genes S and N tend to use a narrower set of synonymous codons that are better optimized to the human host. Conversely, genes E and M consistently use the broader set of synonymous codons, which does not vary in respect to the reference genome. CAI and SiD time evolutions show a tendency to decrease that emerge for most genes. Forsdyke plots are used to study the nature of mutations and they show a rapid evolutionary divergence of each gene, due to the low values of x-intercepets.
Serratia marcescens secretes proteases and chitinases with larvicidal activity against Anopheles dirus

Vector control, the most efficient tool to reduce mosquito-borne disease transmission, has been compromised by the rise of insecticide resistance. Recent studies suggest the potential of mosquito-associated microbiota as a source for new biocontrol agents or new insecticidal chemotypes. In this study, we identified a strain of Serratia marcescens that has larvicidal activity against Anopheles dirus, an important malaria vector in Southeast Asia. This bacterium secretes heat-labile larvicidal macromolecules when cultured under static condition at 25°C but not 37°C. Two major protein bands of approximately 55 kDa and 110 kDa were present in spent medium cultured at 25°C but not at 37°C. The Liquid Chromatography-Mass Spectrometry (LC-MS) analyses of these two protein bands identified several proteases and chitinases that were previously reported for insecticidal properties against agricultural insect pests. The treatment with protease and chitinase inhibitors led to a reduction in larvicidal activity, confirming that these two groups of enzymes are responsible for the macromolecule’s toxicity. Taken together, our results suggest a potential use of these enzymes in the development of larvicidal agents against Anopheles mosquitoes.
Diversity Analysis and Identification of Promising Powdery Mildew Resistance Genotypes in Field Pea (Pisum sativum L.)

In the present study, seventy-one field pea gene pools including three released varieties were evaluated in an augmented block design for assessing genetic divergence and level of resistance to powdery mildew for exploitation in a breeding program aimed at improving yield potential of field pea by using cluster and principal component analysis. Among the 10 studied traits, four (Eigenvalue >1.0) contributed more than 68.45% variability among the materials. Cluster analysis grouped the 71 field pea genotypes into seven distinct classes. The genetic divergence between all possible pairs of clusters were highly significant (P<0.01). The inter-cluster D2 value ranged from 311.63 to 2850.61 indicated that the evaluated gene pools were highly divergent. The genetically more divergent materials present in cluster five and six as indicated by inter-cluster distance value (2850.61). Selecting genotypes of these clusters and crossing them probably provide promising recombinants and better sergeants for future breeding program. Considerable variation was also found for resistance against the powdery mildew diseases. Out of the total 71 genotypes 12 were resistant, 29 were moderately resistant, 25 were moderately susceptible and 5 were susceptible to powdery mildew disease. Among 12 resistant genotypes; GPHA-9 and GPHA-19 were high yielder and GPHA-29, GPHA-48, GPHA-45 and GPHA-42 genotypes were found to be high yielding among 29 moderately resistant genotypes. The resistant genotypes identified could be exploited directly and/or may be transferred through hybridization to high yielding disease susceptible genotypes after checking their yield and disease stability in a number of locations and seasons for more confirmation with the present finding, since the present result was from one location and one season (year) data.
Effect of Height on Perceived Exertion and Physiological Responses for Climbers of Differing Ability Levels

Purpose The purpose of this study was to examine differences in perceived exertion (RPE) and physiological responses for climbers of different abilities completing an identical route low and high above the ground. Materials and Methods Forty-two male (N = 18) and female (N = 24) sport climbers divided into three groups, lower-grade (N = 14), intermediate (N = 14), and advanced climbers (N = 14), completed two visits to a climbing gym, separated by 7 days. In a random order, the climbers completed a close-to-the-ground ascent (treadwall) and climb to height (climbing gym). Immediately after the test, climbers provided their RPE (6–20). Indirect calorimetry was used to assess physiological response during the ascent and recovery. Results The mean (±standard deviation) RPE was higher for lower-grade climbers when ascending the route on the wall (RPE = 12 ± 1) when compared to the treadwall route (RPE = 11 ± 1, P = 0.040; d = 0.41). For all ability groups, the physiological response was higher on the climbing gym wall as opposed to the treadwall: ventilation (P = 0.003, ηp2 = 0.199), heart rate (HR) (P = 0.005, ηp2 = 0.189), energy cost (EC) (P = 0.000, ηp2 = 0.501). The RPE demonstrated a moderate relationship with physiological variables (R2 = 0.14 to R2 = 0.45). Conclusion Climbing to height induced a greater metabolic stress than climbing at a low height (treadwall) and led to higher RPE for lower-grade climbers. In this study, RPE appeared to be a good proxy measure of the physiological demands for advanced climbers but not for intermediate and lower-grade climbers. Therefore, using RPE in climbing with less experienced athletes may perhaps overestimate actual exercise intensity and should be interpreted carefully.
Recombinant single‐chain antibodies against s‐Triazines

Recombinant antibody (RAb) technology is expected to play an essential role in future food and environmental immunoanalysis. The RAb approach is not yet, however, considered as a standard method, mainly due to technical reasons. In order to establish a feasible protocol for the production of hapten specific RAbs, the essential steps of the procedure are considered in detail, especially the polymerase chain reaction amplification of antibody coding genes and the utilization of immunomagnetic selection of phages displaying selective RAbs. The synthesis of functional recombinant single‐chain Fv against s‐triazine herbicides is used as an example. Expressed RAbs are characterized by immunoassay. Although RAb‐based calibration curves were shifted toward higher concentrations by one order of magnitude, the cross‐reactivity pattern of RAbs corresponded to the original monoclonal antibodies. Sequences of different RAb clones derived from the same hybridoma line only differed in a single silent mutation. This conf.
Bacterial Lysates as Immunotherapies for Respiratory Infections: Methods of Preparation

Bacterial lysates, prepared from the microorganisms most frequently involved in human Respiratory Tract Infections (RTIs) have been in the market for several decades, and at present, several different brands are available in many countries worldwide. They all claimed to exert local and systemic immunomodulatory effects but different clinical trials show disparate results between them. The lack of consistency of predicted therapeutic effects has undermined their clinical use and hampered licensing in several countries. One explanation for such lack of consistency in the results is that their methods of preparation are also very different. Here, we review the available literature describing methods of preparation of bacterial lysates, including patent disclosure documents. We found a great variety of methodologies of preparation and a lack of standardized procedures among them. The main conclusion of our study is that there is a clear need for standardized protocols of production to obtain comparable results in clinical trials worldwide.
Electronic Fraud and Performance of Deposit Money Banks in Nigeria: 2008-2018

This research work examined electronic fraud and performance of Deposit Money Banks in Nigeria. It is a truism that Nigerian banks have lost of a lot of profit owing to the nefarious activities of fraudulent people including some unscrupulous elements in the banking industry who connive with fraudsters to perpetrate fraud of different magnitude. To this end, the Central Bank of Nigeria in conjunction with Nigeria Bankers Committee established Nigeria Electronic Fraud Forum (NeFF) with the sole aim of monitoring online banks transactions and reporting any financial regulation infringements. Specifically, the objectives of this research work are to analyse the relationship between ATM fraud and performance of DMBs in Nigeria and to evaluate the relationship between POS fraud and performance of DMBs in Nigeria. The data collected were analyzed using basic descriptive ordinary least square (OLS) and multivariate regression panel data setting with econometric analyses. The results showed negative and insignificant relationship between electronic fraud channels and financial performance variables. The study concluded that there is no significant relationship between electronic fraud and financial performance of Deposit Money Banks in Nigeria in the period of study. The study recommended improved collaborations between DMBs, CBN and other stake holders via NeFF to tackle fraud.
Curiosity, latent learning, and cognitive maps

Curiosity refers to a desire for information that is not driven by immediate strategic or instrumental concerns. Latent earning refers to a form of learning that is not directly driven by standard reinforcement learning processes. We propose that curiosity serves the purpose of motivating latent learning. Thus, while latent learning is often treated as an incidental or passive process, in practice it most often reflects a strong evolved pressure to consume large amounts of information. That large volume of information in turn allows curious decision makers to generate sophisticated representations of the structure of their environment, known as cognitive maps. Cognitive maps facilitate adaptive and flexible behavior while maintaining its adaptivity and flexibility via map updates based on new information. Here we describe data supporting the idea that orbitofrontal cortex (OFC) and dorsal anterior cingulate cortex (dACC) play complementary roles in curiosity-driven learning. Specifically, we propose that (1) OFC tracks the innate value of information and incorporates new information into a detailed cognitive map; and (2) dACC tracks the environmental demands and information availability to then use the cognitive map for guiding behavior.
Genetic and Functional Analyses of Virulence Potential of an Escherichia coli O157:H7 Strain Isolated From Super-Shedder Cattle

Shiga toxin (Stx)-producing Escherichia coli (STEC) O157:H7 is an enteric pathogen that causes life-threatening disease in humans, with cattle being major natural reservoirs. A group of STEC O157:H7 with a dramatic combination of high virulence potentials and super-shedder bovine origin have been isolated. Here, an STEC O157:H7 isolate, JEONG-1266, was analyzed by comparative genomics, stx genotyping, and phenotypic analyses. The phylogenetic typing and whole-genome comparison consistently showed that JEONG-1266 is genetically close to EC4115 (one of 2006 Spinach outbreak isolates) and SS17 (an isolate from super-shedder cattle) strains, all of which belong to lineage I/II and Clade 8. Both lineage I/II and Clade 8 are known to be mostly associated with clinical strains with high virulence and severe clinical symptoms. Further, JEONG-1266, like EC4115 and SS17, harbors stx2a/stx2c genes, and carries Stx-encoding prophages, specifically the φstx2a-γ subtype. Possession of the φstx2a-γ subtype of Stx-encoding prophages and production of Stx2a have been shown to be a key signature associated with hypervirulent STEC O157:H7 strains. In silico virulence typing elucidated JEONG-1266, EC4115, and SS17 shared a highly conserved profile of key virulence genes at the nucleotide sequence level. Consistently, phenotypic data showed that JEONG-1266 expressed a high level of Stx2 toxins and had the full capacity of adhesion in vitro. Taken together, our study suggests that JEONG-1266 may represent an emerging STEC O157:H7 group, which are hypervirulent strains that originate from super-shedders, that can be a threat to food safety and public health.