Miracle-dz/UniFAR-FTUs huggingface dataset:
Whole-Genome Sequence of Aeromonas hydrophila CVM861 Isolated from Diarrhetic Neonatal Swine

Aeromonas hydrophila are ubiquitous in the environment and are highly distributed in aquatic habitats. They have long been known as fish pathogens but are opportunistic human pathogens. Aeromonas spp. have persisted through food-processing safeguards and have been isolated from fresh grocery vegetables, dairy, beef, pork, poultry products and packaged ready-to-eat meats, thus providing an avenue to foodborne illness. A beta-hemolytic, putative Escherichia coli strain collected from diarrheic neonatal pigs in Oklahoma was subsequently identified as A. hydrophila, and designated CVM861. Here we report the whole-genome sequence of A. hydrophila CVM861, SRA accession number, SRR12574563; BioSample number, SAMN1590692; Genbank accession number SRX9061579. The sequence data for CVM861 revealed four Aeromonas-specific virulence genes: lipase (lip), hemolysin (hlyA), cytonic enterotoxin (ast) and phospholipid-cholesterolacyltransferase (GCAT). There were no alignments to any virulence genes in VirulenceFinder. CVM861 contained an E. coli resistance plasmid identified as IncQ1_1__M28829. There were five aminoglycoside, three beta-lactam, and one each of macrolide, phenicol, sulfonamide, tetracycline and trimethoprim resistance genes, all with over 95% identity to genes in the ResFinder database. Additionally, there were 36 alignments to mobile genetic elements using MobileElementFinder. This shows that an aquatic pathogen, rarely considered in human disease, contributes to the resistome reservoir and may be capable of transferring resistance and virulence genes to other more prevalent foodborne strains such as E. coli or Salmonella in swine or other food production systems.
Sport Practice Enhances Athletes’ Observation Capacity: Comparing Scenic Change Detection in Open and Closed Sports

Domain-specific knowledge guides our attention and thus influences our perception. Prior change-blindness research has shown that expert athletes can spot meaningful scene changes more quickly than novices, but less is known of whether this expertise is modulated differentially between open and closed sporting activities. We presented 81 individuals (20 gymnasts, 19 rock climbers, 22 parkour practitioners, and 20 control participants) with alternating sequences of images that corresponded to the habitual training landscapes of each group (gymnasiums, rock cliffs, and urban environments, respectively). We included contextual and non-contextual scenic changes to evaluate whether athletes were generally aware of their environments, or whether their observation strategies only targeted sport-related environmental elements. Among these three athletic endeavors, we found that gymnasts were faster at detecting changes in their environment, irrespective of whether or not these changes were contextual to the sports involved. Expert rock climbers presented a domain-specific expertise that was improved even further for contextual changes. Parkour practitioners presented the fastest reaction times in the urban environment and some of the best reaction times for all types of changes. These results confirm that an ability to read the environment is an integral aspect of practice in open-skilled sports, while skills of athletes in closed-skilled sports are more closely related to motor skill repetitions in constant environments. Thus, open skill training may benefit athletes’ guidance of attention. Our finding that parkour practitioners appeared to have developed the widest perceptual abilities was probably linked to these athletes’ extremely wide range of practice environments and with the constant demands of this sport to find solutions in random natural environments that that are not purposely designed for the sport.
Molecular diversity of coronavirus host cell entry receptors

ABSTRACT Coronaviruses are a group of viruses causing disease in a wide range of animals, and humans. Since 2002, the successive emergence of bat-borne severe acute respiratory syndrome coronavirus (SARS-CoV), Middle East respiratory syndrome coronavirus (MERS-CoV), swine acute diarrhea syndrome coronavirus (SADS-CoV) and SARS-CoV-2 has reinforced efforts in uncovering the molecular and evolutionary mechanisms governing coronavirus cell tropism and interspecies transmission. Decades of studies have led to the discovery of a broad set of carbohydrate and protein receptors for many animal and human coronaviruses. As the main determinant of coronavirus entry, the spike protein binds to these receptors and mediates membrane fusion. Prone to mutations and recombination, spike evolution has been studied extensively. The interactions between spike proteins and their receptors are often complex and despite many advances in the field, there remains many unresolved questions concerning coronavirus tropism modification and cross-species transmission, potentially leading to delays in outbreak responses. The emergence of SARS-CoV-2 underscores the need to address these outstanding issues in order to better anticipate new outbreaks. In this review, we discuss the latest advances in the field of coronavirus receptors emphasizing on the molecular and evolutionary processes that underlie coronavirus receptor usage and host range expansion.
Mechanisms Affecting the Acquisition, Persistence and Transmission of Francisella tularensis in Ticks

Over 600,000 vector-borne disease cases were reported in the United States (U.S.) in the past 13 years, of which more than three-quarters were tick-borne diseases. Although Lyme disease accounts for the majority of tick-borne disease cases in the U.S., tularemia cases have been increasing over the past decade, with >220 cases reported yearly. However, when comparing Borrelia burgdorferi (causative agent of Lyme disease) and Francisella tularensis (causative agent of tularemia), the low infectious dose (<10 bacteria), high morbidity and mortality rates, and potential transmission of tularemia by multiple tick vectors have raised national concerns about future tularemia outbreaks. Despite these concerns, little is known about how F. tularensis is acquired by, persists in, or is transmitted by ticks. Moreover, the role of one or more tick vectors in transmitting F. tularensis to humans remains a major question. Finally, virtually no studies have examined how F. tularensis adapts to life in the tick (vs. the mammalian host), how tick endosymbionts affect F. tularensis infections, or whether other factors (e.g., tick immunity) impact the ability of F. tularensis to infect ticks. This review will assess our current understanding of each of these issues and will offer a framework for future studies, which could help us better understand tularemia and other tick-borne diseases.
Parks for sharks: human exclusion areas outperform no‐take marine reserves

We collected reef shark population data from a large network of no-take and no-entry reserves (ie human exclusion areas), as well as from fished reefs, in one of the world's most intensively managed marine parks - the Great Barrier Reef of Australia. The sampled reserves have been protected for varying lengths of time, making it possible to use space-for-time chronosequences to infer recovery trajectories of reef shark populations after extractive use is banned, and to compare the effectiveness of shark population recovery in no-take and no-entry reserves. After 20- 40 years of protection, density and biomass of sharks in no-entry reserves approached asymptotes (ie plateaus) that were more than double and triple, respectively, those in no-take reserves. These results not only indicate that restoration of near-natural shark populations requires multidecadal time frames, but also clearly demonstrate the superior performance of no-entry reserves in terms of rebuilding shark populations. Ongoing poaching in no-take reserves, which are more difficult for law enforcement to police than no-entry reserves, is the probable cause of the disparity. Given the ubiquitous use of no-take reserves as ecological baselines and the potentially pervasive trophic effects of removing large predators, we argue that current perceptions of the structure and function of natural reef ecosystems may be skewed, which has broad implications for science and management of marine ecosystems.
Transcervical Access for Endograft Exclusion of a Postendarterectomy Carotid Pseudoaneurysm in a Patient With Type III Aortic Arch

Postendarterectomy carotid pseudoaneurysms are infrequent. The endovascular treatment is less invasive, with a minor risk of complications. However, the presence of a highly angulated aortic arch (type III) is a challenge, since the navigation of endovascular devices is not favorable. Through transcervical access, it is possible to deliver the devices directly into the carotid artery. We herein present a case of a postendarterectomy carotid pseudoaneurysm in a patient with type III aortic arch that was successfully treated with transcervical endograft exclusion.
Mammalian kinetochores count attached microtubules in a sensitive and switch-like manner to control cell cycle progression

The Spindle Assembly Checkpoint (SAC) maintains genomic integrity by preventing anaphase until all kinetochores attach to the spindle. What specific signals are required for SAC satisfaction at mammalian kinetochores, and in what magnitude, are not well understood and central to understanding SAC signal processing and function. Here, we directly and independently tune candidate input signals – spindle forces and Hec1-microtubule binding – and map SAC outputs. By detaching microtubules from the spindle, we first demonstrate that the SAC does not respond to changes in spindle pulling forces. We then tune and fix the fraction of Hec1 molecules capable of microtubule binding, and interpret SAC output changes as coming from changes in binding, and not spindle forces. While the speed of satisfaction reduces with fewer attached microtubules, the kinetochore turns off the SAC even with few – approximately four – such microtubules. Thus, the mammalian kinetochore responds specifically to microtubule binding, and does so as a single, switch-like, sensitive unit. This may allow the kinetochore to rapidly react to attachments and maintain a robust response despite dynamic microtubule numbers.
Mechanism of Probiotics in the Colon Cancer Treatment

Probiotic bacteria has been found to exert anti-tumour effects against colon cancer. The possible mechanisms of probiotics in prevention and treatment of colon cancer include adjusting intestinal flora, regulating microflora metabolites, maintaining intestinal homeostasis, inducing immune regulation, antioxidant activity, inducing apoptosis and anti-inflammation.
Longitudinal Changes of Deep and Surface Learning in a Constructivist Pharmacy Curriculum

In the undergraduate Pharmacy program at the department of Pharmaceutical Sciences, Utrecht University, an educational model is used that is aimed at the development of deep and self-regulating learning. It is, however, unknown whether these objectives are realized. The aim of this study was to assess longitudinal changes in processing and regulation strategies of student learning during their progression in the curriculum, that is explicitly based on constructivist principles. Processing strategies (deep vs. stepwise), regulation strategies (self- vs. external), conceptions of learning and orientations to learning were measured with the Inventory of Learning patterns of Students (ILS). Longitudinal data are reported here for students, of which data are available for year 1/2 and year 4/5 (n = 90). The results demonstrate that the use of deep processing (critical thinking in particular, effect size = 0.94), stepwise processing (analyzing in particular, effect size = 0.55) and concrete processing strategies (effect size = 0.78) increases between the bachelor phase (year 1/2) and the master phase (year 4/5). This change is based on the students having a constructivist view about the nature of learning and is mediated through a relatively large increase in the use of self-regulating strategies (effect size = 0.75). We conclude that this six-year undergraduate Pharmacy program effectively stimulates the development of deep and self-regulated learning strategies in pharmacy students.
Design and Analysis of a Variable Inertia Spatial Robotic Tail for Dynamic Stabilization

This paper presents the design of a four degree-of-freedom (DoF) spatial tail and demonstrates the dynamic stabilization of a bipedal robotic platform through a hardware-in-loop simulation. The proposed tail design features three active revolute joints with an active prismatic joint, the latter of which provides a variable moment of inertia. Real-time experimental results validate the derived mathematical model when compared to simulated reactive moment results, both obtained while executing a pre-determined trajectory. A 4-DoF tail prototype was constructed and the tail dynamics, in terms of reactive force and moments, were validated using a 6-axis load cell. The paper also presents a case study where a zero moment point (ZMP) placement-based trajectory planner, along with a model-based controller, was developed in order for the tail to stabilize a simulated unstable biped robot. The case study also demonstrates the capability of the motion planner and controller in reducing the system’s kinetic energy during periods of instability by maintaining ZMP within the support polygon of the host biped robot. Both experimental and simulation results show an improvement in the tail-generated reactive moments for robot stabilization through the inclusion of prismatic motion while executing complex trajectories.
Pengaruh Pemberian Coklat (Theobroma cacao) terhadap Kualitas Spermatozoa Tikus Wistar (Rattus norvegicus) yang Terpapar Stres

Abstract: A chocolate compound, flavonoid which is a subgroup of polyphenols, has protective effect on spermatozoa exposed to stress. The flavonoid compound in chocolate, (-)-epicatehin, plays important roles in neutralizing ROS, blocking the production of ROS, and inhibiting enzyme activity of DNA methyltransferase. Stress activates the hypothalamus-pituitary-adrenal (HPA) and simpatoadrenomedular systems that have glucocorticoid as their end product that can cause an increase in essential catabolism and trigger the production of ROS. Oxidative stress can reduce the motility of spermatozoa and cause damage to DNA of spermatozoa. This study was aimed to determine the effect of chocolate (Theobroma cacao) on the quality of spermatozoa in stressed Wistar rats (Rattus norvegicus). This was an experimental study with a post-test only control group design. Samples were spermatozoa of Wistar rats. There were 9 Wistar rats divided into 3 groups, as follows: P0 (control), P1 (stress treatment only), and P2 (stress treatment and chocolate administration). The results showed that there were no significant differences in concentration and motility, albeit, there was a significant difference in morphology of spermatozoa in Wistar rats (Rattus norvegicus). Conclusion: Chocolate (Theobroma cacao) can influence the increase of morphologic quality of spermatozoa in stressed Wistar rats.Keywords: chocolate, stress, spermatozoa Abstrak: Kandungan coklat, yaitu flavonoid merupakan subgrup dari polifenol yang memiliki efek protektif terhadap spermatozoa dari paparan stres. Jenis flavonoid dalam coklat, (-)-epicatehin berperan dalam menetralisir ROS, memblokir produksi ROS, dan menginhibisi aktivitas enzim DNA methyltransferase. Stres mengaktifkan sistem hipotalamus-pituitari-adrenal (HPA) dan simpatoadrenomedular yang memiliki produk akhir glukokortikoid yang dapat menyebabkan peningkatan katabolisme esensial dan memicu produksi ROS. Stres oksidatif dapat menurunkan motilitas spermatozoa dan menyebabkan kerusakan DNA spermatozoa. Penelitian ini bertujuan untuk mengetahui pengaruh pemberian coklat (Theobroma cacao) terhadap kualitas spermatozoa tikus Wistar (Rattus norvegicus) yang terpapar stres. Jenis penelitian ialah eksperimental dengan post-test only control group design. Sampel penelitian ialah spermatozoa tikus Wistar (Rattus norvegicus). Dilakukan perlakuan terhadap 9 ekor tikus Wistar yang dibagi menjadi 3 kelompok, yaitu P0 (kontrol), P1 (perlakuan stres saja), dan P2 (perlakuan stres dan pemberian coklat). Hasil penelitian tidak mendapatkan perbedaan bermakna pada konsentrasi dan motilitas tetapi terdapat perbedaan bermakna pada morfologi spermatozoa tikus Wistar (Rattus norvegicus). Simpulan: Pemberian coklat (Theobroma cacao) berpengaruh terhadap peningkatan kualitas morfologi spermatozoa tikus Wistar (Rattus norvegicus) yang terpapar stres.Kata kunci: coklat, stres, spermatozoa
Association of paired box 9 (PAX9) (rs12881240) and muscle segment homeobox 1(MSX1) (rs12532) gene polymorphisms in human tooth agenesis

Agenesis of one or more teeth is the most common anomaly observed in human craniofacial development. The aim is to test the association between PAX9 (rs12881240) and MSX1 (rs12532) polymorphisms and tooth agenesis in local population. DNA samples of 25 subjects with non-syndromic tooth agenesis and 25 unrelated controls, collected from the department were used for the study. The extracted DNA samples were subjected to Polymerase chain reaction and then subjected to DNA sequencing. This study also suggests that the likelihood of Non syndromic tooth agenesis is higher in subjects having CT (p=0.02) genotype of PAX 9 gene variant rs12881240 & AG (p=0.02) genotype for MSX 1 gene variant rs12532. Conclusion is the PAX 9 gene variant rs12881240 and MSX 1 gene variant rs12532 can be considered as genetic markers for Non-syndromic Tooth agenesis in local population.
K-Ras–Activated Cells Can Develop into Lung Tumors When Runx3-Mediated Tumor Suppressor Pathways Are Abrogated

K-RAS is frequently mutated in human lung adenocarcinomas (ADCs), and the p53 pathway plays a central role in cellular defense against oncogenic K-RAS mutation. However, in mouse lung cancer models, oncogenic K-Ras mutation alone can induce ADCs without p53 mutation, and loss of p53 does not have a significant impact on early K-Ras–induced lung tumorigenesis. These results raise the question of how K-Ras–activated cells evade oncogene surveillance mechanisms and develop into lung ADCs. RUNX3 plays a key role at the restriction (R)-point, which governs multiple tumor suppressor pathways including the p14ARF–p53 pathway. In this study, we found that K-Ras activation in a very limited number of cells, alone or in combination with p53 inactivation, failed to induce any pathologic lesions for up to 1 year. By contrast, when Runx3 was inactivated and K-Ras was activated by the same targeting method, lung ADCs and other tumors were rapidly induced. In a urethane-induced mouse lung tumor model that recapitulates the features of K-RAS–driven human lung tumors, Runx3 was inactivated in both adenomas (ADs) and ADCs, whereas K-Ras was activated only in ADCs. Together, these results demonstrate that the R-point–associated oncogene surveillance mechanism is abrogated by Runx3 inactivation in AD cells and these cells cannot defend against K-Ras activation, resulting in the transition from AD to ADC. Therefore, K-Ras–activated lung epithelial cells do not evade oncogene surveillance mechanisms; instead, they are selected if they occur in AD cells in which Runx3 has been inactivated.
Pseudocholinesterase and its relationship to serum lipoproteins in diabetes mellitus

The activities of pseudocholinesterase (PChE) were compared in the serum of type I and type II diabetic patients and non-diabetic subjects. Both type I and type II diabetic patients showed increased serum PChE activity concomitant with the presence of hyperlipidemia. Pearsons correlation analysis showed a positive correlation between triglycerides (TG) and PChE in both type I (P=0.499) and type II (P=0.526) diabetic patients. -- Induction of chemical diabetes in rats with Streptozotocin (SZ) and alloxan also increased the serum PChE activity which paralleled the development of diabetes mellitus. Serum triglycerides, apo-B containing lipoproteins (total low density lipoproteins TLDL) and glycerol concentrations also increased. When the hyperglycemia produced in streptozotocin induced diabetic rats was controlled by administration of insulin, the levels of TG, glycerol and PChE activity all reverted to pre-diabetic levels. When insulin treatment was withdrawn hyperglycemia developed again and serum levels of PChE activity, TG, glycerol and TLDL also increased. The concentration of TG in the liver of SZ-diabetic rats was significantly higher compared to the normal rats. Adipose tissue and liver PChE activity were not significantly different in these SZ-diabetic rats. -- Gold thioglucose (GTG) treated mice, which are type II diabetic models, also showed a significant increase in serum PChE activity and lipids similar to the SZ induced type I diabetic models. Inhibition of PChE activity in GTG treated mice was associated with a decrease in serum glycerol, TG and TLDL levels. Liver PChE activity was markedly higher in the GTG treated mice compared to the untreated control mice. Administration of Iso-OMPA to GTG treated mice inhibited both liver and adipose tissue PChE activity. -- Heparin treatment of SZ-diabetic rats significantly reduced serum TG levels without affecting PChE activity, cholesterol, HDL-C or TLDL levels. -- Administration of Iso-OMPA, a specific PChE inhibitor, to SZ-diabetic and normal rats produced a significant reduction in serum TG, glycerol and TLDL levels. Withdrawal of iso-OMPA inhibition in the diabetic rats resulted in an increase in the lipid levels to those previously present in the diabetic state. PChE activity and TG levels were also reduced in the iso-OMPA treated diabetic and normal rat livers compared to the untreated rats. Adipose tissue PChE activity was also inhibited in the iso-OMPA treated diabetic and normal rat. -- Inhibition of PChE activity with iso-OMPA failed to produce an accumulation of choline or cholinesters in the liver, serum or to affect their excretion in the urine of normal rats. -- The results indicate that changes in PChE activity parallel changes in TG metabolism, particularly during the perturbances that accompany diabetes mellitus. Whether PChE has a role in very low density TG (VLDL-TG) metabolism remains to be determined but is of considerable interest.
New Insights into Therapy-Induced Progression of Cancer

The malignant tumor is a complex heterogeneous set of cells functioning in a no less heterogeneous microenvironment. Like any dynamic system, cancerous tumors evolve and undergo changes in response to external influences, including therapy. Initially, most tumors are susceptible to treatment. However, remaining cancer cells may rapidly reestablish the tumor after a temporary remission. These new populations of malignant cells usually have increased resistance not only to the first-line agent, but also to the second- and third-line drugs, leading to a significant decrease in patient survival. Multiple studies describe the mechanism of acquired therapy resistance. In past decades, it became clear that, in addition to the simple selection of pre-existing resistant clones, therapy induces a highly complicated and tightly regulated molecular response that allows tumors to adapt to current and even subsequent therapeutic interventions. This review summarizes mechanisms of acquired resistance, such as secondary genetic alterations, impaired function of drug transporters, and autophagy. Moreover, we describe less obvious molecular aspects of therapy resistance in cancers, including epithelial-to-mesenchymal transition, cell cycle alterations, and the role of intercellular communication. Understanding these molecular mechanisms will be beneficial in finding novel therapeutic approaches for cancer therapy.