Miracle-dz/UniFAR-FTUs huggingface dataset:
Inference and dynamic simulation of malaria using a simple climate-driven entomological model of malaria transmission

Given the crucial role of climate in malaria transmission, many mechanistic models of malaria represent vector biology and the parasite lifecycle as functions of climate variables in order to accurately capture malaria transmission dynamics. Lower dimension mechanistic models that utilize implicit vector dynamics have relied on indirect climate modulation of transmission processes, which compromises investigation of the ecological role played by climate in malaria transmission. In this study, we develop an implicit process-based malaria model with direct climate-mediated modulation of transmission pressure borne through the Entomological Inoculation Rate (EIR). The EIR, a measure of the number of infectious bites per person per unit time, includes the effects of vector dynamics, resulting from mosquito development, survivorship, feeding activity and parasite development, all of which are moderated by climate. We combine this EIR-model framework, which is driven by rainfall and temperature, with Bayesian inference methods, and evaluate the model’s ability to simulate local transmission across 42 regions in Rwanda over four years. Our findings indicate that the biologically-motivated, EIR-model framework is capable of accurately simulating seasonal malaria dynamics and capturing of some of the inter-annual variation in malaria incidence. However, the model unsurprisingly failed to reproduce large declines in malaria transmission during 2018 and 2019 due to elevated anti-malaria measures, which were not accounted for in the model structure. The climate-driven transmission model also captured regional variation in malaria incidence across Rwanda’s diverse climate, while identifying key entomological and epidemiological parameters important to seasonal malaria dynamics. In general, this new model construct advances the capabilities of implicitly-forced lower dimension dynamical malaria models by leveraging climate drivers of malaria ecology and transmission.
Doublecortin immunolabeling and lack of neuronal nuclear protein immunolabeling in feline gliomas

Doublecortin (DCX) and neuronal nuclear protein (NeuN) can be used as immunomarkers of neuronal progenitor cells and mature neurons, respectively. Increased DCX immunolabeling has been associated with tumor invasion in human gliomas and anaplastic canine meningiomas. These immunomarkers have not been assessed in feline gliomas. Here we characterized the DCX and NeuN immunohistochemistry (IHC) profile in 11 feline gliomas (7 oligodendrogliomas, 4 astrocytomas). Immunolabeling was classified according to intensity (weak, moderate, strong), distribution of neoplastic cell immunolabeling (1 = <30%, 2 = 30–70%, 3 = >70%), and predominant location within the neoplasm (random or at tumor margins). DCX immunolabeling was strong in 6 cases, weak in 4 cases, and moderate in 1 case. The distribution of DCX immunolabeling was characterized as 1 (4 cases), 2 (4 cases), and 3 (3 cases). DCX immunolabeling occurred predominantly in astrocytomas, which had stronger immunostaining at the tumor margins. NeuN immunolabeling was absent in all cases. Our IHC findings are similar to those reported for DCX and NeuN IHC in canine gliomas. The increased DCX immunolabeling at tumor margins is similar to labeling in invasive human gliomas and anaplastic canine meningiomas.
Properties of superconducting microbridges in the pure limit

An exact solution of Eilenberger's equations for a superconducting microbridge in the limit avery-much-less-thanxi/sub 0/, avery-much-less-thanl is given (a is the radius of the constriction between the superconductors, l is the mean free path and xi/sub 0/ is the coherence length). The current is independent of the ratio between l xi/sub 0/ and is expressed in terms of the contact resistance in the normal state. When T=0, the magnitude of the critical current exceeds the critical current of the tunnel contact with the same resistance, by a factor of two.
Prospects for the use of macrocyclic photosensitizers for inactivation of SARS-CoV-2: selection of compounds leaders based on the molecular docking data

Abstract The treatment of coronavirus COVID-19, like other viral diseases, is currently underdeveloped. This fact necessitates the search for new drugs and treatment methods that will effectively disrupt the life cycle of the virus. A big problem in the therapy of viral diseases is the ability of viruses to evade the host's immune response. We suppose that the search for drugs that can change the evasiveness of the virus from the immune response of the host is a very promising strategy, as it can help the body to cope with the infection. Protein SARS-CoV-2 ORF8 is one of the key proteins that can suppress antiviral immunity. This paper considers the available information on the structure and functioning of ORF8, as well as the results of molecular docking of ORF8 to a wide range of tetrapyrrole macroheterocyclic compounds capable of generating reactive oxygen species upon photoirradiation. This principle of photoinactivation of biosubstrates underlies the methods of photodynamic therapy of cancer. Application of photoinactivation of drug-resistant forms of bacteria and some viruses can be useful in the fight against COVID-19 and other viral infections. In this work, the structure of ORF8 complexes with macrocyclic compounds is considered in detail, the dependence of their binding affinity on the nature of macrocycles and the nature of peripheral substituents is analyzed and spectral studies of the binding of ORF8 to chlorin is performed. This paper is a part of a large project to investigate the possibility of using macrocyclic compounds for the treatment of viral diseases. Communicated by Ramaswamy H. Sarma
Closed, Circular Genome Sequence of Aureococcus anophagefferens Virus, a Lytic Virus of a Brown Tide-Forming Alga

Here, we report the genomic sequence of Aureococcus anophagefferens virus, assembled into one circular contig from both Nanopore and Illumina reads. The genome is 381,717 bp long with a GC content of 29.1%, which includes an additional 5-kb region between the previously predicted polar ends of the reference genome. ABSTRACT Here, we report the genomic sequence of Aureococcus anophagefferens virus, assembled into one circular contig from both Nanopore and Illumina reads. The genome is 381,717 bp long with a GC content of 29.1%, which includes an additional 5-kb region between the previously predicted polar ends of the reference genome.
Spatiotemporal analysis of cutaneous leishmaniasis in Palestine and foresight study by projections modelling until 2060 based on climate change prediction

Background Cutaneous leishmaniasis (CL) is a vector-borne parasitic diseases of public health importance that is prevalent in the West Bank but not in the Gaza Strip. The disease caused by parasitic protozoans from the genus Leishmania and it is transmitted by infected phlebotomine sand flies. The aim of our study is to investigate the eco-epidemiological parameters and spatiotemporal projections of CL in Palestine over a 30-years period from 1990 through 2020 and to explore future projections until 2060. Methodology/Principal findings This long-term descriptive epidemiological study includes investigation of demographic characteristics of reported patients by the Palestinian Ministry of Health (PMoH). Moreover, we explored spatiotemporal distribution of CL including future projection based on climate change scenarios. The number of CL patients reported during this period was 5855 cases, and the average annual incidence rate (AAIR) was 18.5 cases/105 population. The male to female ratio was 1.25:1. Patients-age ranged from 2 months to 89 years (mean = 22.5, std 18.67, and the median was 18 years). More than 65% of the cases came from three governates in the West Bank; Jenin 29% (1617 cases), Jericho 25% (1403), and Tubas 12% (658) with no cases reported in the Gaza Strip. Seasonal occurrence of CL starts to increase in December and peaked during March and April of the following year. Current distribution of CL indicate that Jericho, Tubas, Jenin and Nablus have the most suitable climatic settings for the sandfly vectors. Future projections until 2060 suggest an increasing incidence from northwest of Jenin down to the southwest of Ramallah, disappearance of the foci in Jericho and Tubas throughout the Jordan Vally, and possible emergence of new foci in Gaza Strip. Conclusions/Significance The future projection of CL in Palestine until 2060 show a tendency of increasing incidence in the north western parts of the West Bank, disappearance from Jericho and Tubas throughout the Jordan Vally, and emergence of new CL endemic foci in the Gaza Strip. These results should be considered to implement effective control and surveillance systems to counteract spatial expansion of CL vectors.
Response to “Methodological issues in the designing and reporting of frequentist and Bayesian meta‐analysis to assess COVID‐19 outcomes among PLHIV with various comorbidities” by Ram Bajpai, Vivek Verma and Gyan Prakash Singh

Response to “Methodological issues in the designing and reporting of frequentist and Bayesian meta-analysis to assess COVID-19 outcomes among PLHIV with various comorbidities” by Ram Bajpai, Vivek Verma and Gyan Prakash Singh Haoyi Wang and Kai J. Jonas§ §Corresponding author: Kai J. Jonas, Department of Work and Social Psychology, Maastricht University, Maastricht 6200ER, The Netherlands. Tel: +31 43 38 84068. (kai.jonas@maastrichtuniversity.nl)
TIF1α mediates physical interaction and functional synergy between the CARM1 and GRIP1 nuclear receptor coactivators

In previous studies Transcriptional Intermediary Factor 1α (TIF1α) was identified as a direct binding partner and potential transcriptional coactivator for nuclear receptors (NR), but its over-expression inhibited rather than enhanced transcriptional activation by NRs. Here we show that TIF1α bound to and enhanced the function of the C-terminal activation domain of Coactivator Associated Arginine Methyltransferase 1 (CARM1) and the N-terminal activation domain of Glucocorticoid Receptor Interacting Protein 1 (GRIP1). Furthermore, although TIF1α had little or no NR coactivator activity by itself, it cooperated synergistically with GRIP1 and CARM1 to enhance NR-mediated transcription. Inhibition of endogenous TIF1α expression reduced transcriptional activation by the GRIP1 N-terminal domain but not by the CARM1 C-terminal domain, suggesting that TIF1α may be more important for mediating the activity of the former than the latter. Reduction of endogenous TIF1α levels also compromised the androgen-dependent induction of an endogenous target gene of the androgen receptor. Finally, TIF1α formed a ternary complex with the GRIP1 N-terminal and CARM1 C-terminal domains. Thus, we conclude that TIF1α cooperates with NR coactivators GRIP1 and CARM1 by forming a stable ternary complex with them and enhancing the activation domain function of one or both of them.
Dissociating Statistically–Determined Alzheimer/Vascular Dementia Neuropsychological Syndromes Using White and Gray Neuroradiological Parameters

Objectives—To use statistical modeling of neuropsychological data to determine subgroups of dementia patients clinically diagnosed with Alzheimer’s disease (AD) or vascular dementia (VaD) and then, using brain imaging, investigate between group differences in gray and white matter regions of interest. Methods—An analysis of neuropsychological functioning was obtained from dementia patients clinically diagnosed with AD/VaD characterized with significant leukoaraiosis (LA) and/or lacunes where a k-means cluster analysis requested a 3-group solution. MRI measures of hippocampal, caudate, ventricular, subcortical lacunar infarction, whole brain volume and LA were analyzed. Three regions of LA volumes were quantified and these included the periventricular (5mm around the ventricles), infracortical (5mm beneath the gray matter), and deep (between periventricular and infracortical) regions. Results—Cluster analysis sorted AD/VaD patients into single domain amnestic (n=41), singledomain dysexecutive (n=26), and multi-domain (n=26) phenotypes. The multi-domain patients exhibited worst performance on language tests; however, multi-domain patients were equally impaired on memory tests when compared to amnestic patients. Statistically-determined groups were relatively dissociated using neuroradiological parameters such that amnestic and multiCorrespondence: Catherine C. Price, Ph.D., ABPP/Cn, Associate Professor, Clinical and Health Psychology, 101 S. Newell Drive, PO Box 100165, University of Florida, 32610, cep23@phhp.ufl. edu (v) 352-273-5929, (f) 352-265-0096 or David J. Libon, Professor, Neurology, Drexel University; djlibon@drexelmed.edu. Author Contributions: Price, C. C. – study concept, study supervision/coordination, data acquisition, analysis and interpretation, writing manuscript drafts, securing funding; Tanner, J.J. – acquisition of data and revision of drafts; Schmalfuss, I. – study design, revision of drafts; Heilman, K.M. – study concept, revision of draft; Libon, D.J. – study concept, analysis and interpretation, writing manuscript drafts, securing funding. HHS Public Access Author manuscript J Alzheimers Dis. Author manuscript; available in PMC 2016 January 25. Published in final edited form as: J Alzheimers Dis. 2015 ; 48(3): 833–847. doi:10.3233/JAD-150407. A uhor M anscript
PROP taster status not related to reported cruciferous vegetable intake among ethnically diverse children

Sensitivity to the taste of 6-n-propylthiouracil (PROP) (a bitter tasting chemical related to the phenylthiocarbamide found in cruciferous vegetables) has been related to dietary intake or preferences of cruciferous vegetables among adults and young children, but not middle aged children or adolescents. We hypothesized that PROP taste sensitivity is related to lower reported dietary intake of cruciferous vegetables, primarily among younger children (i.e. a moderating effect of child age). This study examined the relationship of PROP sensitivity to reported dietary intake across three days in two age groups of youth (9–10 years and 17–18 year), while statistically controlling for physical activity, social desirability and reporting bias. Cross sectional design was employed with a multi-ethnic (White, African American, Hispanic, and Other) sample of 843 males and females. Children were recruited from and data were collected in local elementary and high schools that had at least 30% ethnic minority enrollment. Children providing nonplausible reports of dietary intake were deleted from the analyses. BMI was calculated and expressed in z-scores. Energy intake and physical activity were measured by three telephone conducted 24-hour dietary recalls with the Nutrient Data System for Research (NDSR) and 5 days of Actigraph activity monitor. The primary analyses included 347 students. PROP sensitivity was not related to intake of cruciferous vegetables. Intakes of the cruciferous vegetables were low, which may explain the lack of relationship.
Photon-Mediated Thermoelectric and Heat Currents through a Resonant Quantum Wire-Cavity System

We theoretically consider a short quantum wire, which on both ends is connected to leads that have different temperatures. The quantum wire is assumed to be coupled to a cavity with a single-photon mode. We calculate the heat and thermoelectric currents in the quantum wire under the effect of the photon field. In the absence of the photon field, a plateau in the thermoelectric current is observed due to the thermal smearing at a high temperature gradient. In the presence of the resonance photon field, when the energy spacing between the lowest states of the quantum wire is approximately equal to the photon energy, a suppression in thermoelectric current and negativity in the heat current are seen due to the dressed electron-photon states. It is also found that the cavity with high photon energy has more influence on the thermoelectric current at a high temperature gradient.
Detection of circular excised DNA deletion elements in Tetrahymena therrmophila during development

Extensive programmed DNA deletion occurs in ciliates during development. In this study we examine the excised forms of two previously characterized deletion elements, the Rand M-element, in Tetrahymena. Using divergently oriented primers in polymerase chain reactions we have detected the junctions formed by joining the two ends of these elements, providing evidence for the presence of circular excised forms. These circlar forms were detected in developing macronuclear DNA from 12 24 h after mating began, but not in micronuclear or whole cell DNA of vegetative cells. They are present at very low abundance, detectable after PCR only through hybridization with specific probes. Sequence analysis shows that the circle junctions occur at or very near the known ends of the elements. There is sequence microheterogeneity in these junctions, which does not support a simple reciprocal exchange model for DNA deletion. A model involving staggered cuts and variable mismatch repair is proposed to explain these results. This model also explains the sequence microheterogeneity previously detected among the junction sequences retained in the macronuclear chromosome.
THE ABDUS SALAM INTERNATIONAL CENTRE FOR THEORETICAL PHYSICS GENERALIZED TOEPLITZ OPERATORS AND CYCLIC VECTORS

We give in this paper some asymptotic Von Neumann inequalities for power bounded operators in the class Cp Π C\t and some spacial von Neumann inequalities associated with non zero elements of the point spectrum, when it is non void, of generalized Toeplitz operators. Introducing perturbed kernel, we consider classes CR which extend the classical classes Cp. We give results about absolute continuity with respect to the Haar measure for operators in class CR Π (7ι; . This allows us to give new results on cyclic vectors for such operators and provides invariant subspaces for their powers. Relationships between cyclic vectors for Τ and T* involving generalized Toeplitz operators are given and the commutativity of {T}', the commutant of Τ is discussed.
The Chimpanzee VA-B Blood Group System

The chimpanzee V-A-B blood group system [1] was so named because it was determined by tests with two isoimmune sera designated anti-Ae* and anti-Bc (c for chimpanzee), respectively, and by the anti-NV lectin from the seeds of Vicia graminea; contingency tests showed that the three specificities defined by these three reagents were associated with one another. Initially it was thought that eight V-A-B blood types might exist and that as many as eight allelic genes might be required to account for the heredity. However, analysis by the method of population genetics indicated that no more than five alleles were actually needed to account for the observed distribution of the phenotypes. Subsequently, immunization of chimpanzees with human red cells produced a reagent [2] which gave reactions with chimpanzee red cells paralleling those of anti-NV lectin, and therefore, designated as anti-Vc. The production of anti-Ve reagents in chimpanzees alleviated the problem caused by the limited availability of anti-NV lectin and thus facilitated further studies on the V-A-B blood types. The fact that anti-NV lectin detected both the agglutinogen Ve of chimpanzee and the agglutinogen N of human red cells indicated homology between the chimpanzee V-A-B system and the human M-N system. This received further support from the observation that the enzyme ficin destroys the ability of chimpanzee red cells to react with V-A-B as well as M-N reagents [3]. More recently [4], tests with new reagents indicated that the V-A-B types were transmitted by no more than four allelic genes, namely, the codominant alleles V, VA, and vB and the amorph v. Thus, only seven and not eight V-A-B types presumably could exist, and this theory received further support when repeated tests with more potent and specific antisera showed that the single animal previously typed as V.AB actually belonged to type V.A. In addition,
Inner-outer Iterative Methods for Eigenvalue Problems - Convergence and Preconditioning

Many methods for computing eigenvalues of a large sparse matrix involve shift-invert transformations which require the solution of a shifted linear system at each step. This thesis deals with shift-invert iterative techniques for solving eigenvalue problems where the arising linear systems are solved inexactly using a second iterative technique. This approach leads to an inner-outer type algorithm. We provide convergence results for the outer iterative eigenvalue computation as well as techniques for efficient inner solves. In particular eigenvalue computations using inexact inverse iteration, the Jacobi-Davidson method without subspace expansion and the shift-invert Arnoldi method as a subspace method are investigated in detail. A general convergence result for inexact inverse iteration for the non-Hermitian generalised eigenvalue problem is given, using only minimal assumptions. This convergence result is obtained in two different ways; on the one hand, we use an equivalence result between inexact inverse iteration applied to the generalised eigenproblem and modified Newton's method; on the other hand, a splitting method is used which generalises the idea of orthogonal decomposition. Both approaches also include an analysis for the convergence theory of a version of inexact Jacobi-Davidson method, where equivalences between Newton's method, inverse iteration and the Jacobi-Davidson method are exploited. To improve the efficiency of the inner iterative solves we introduce a new tuning strategy which can be applied to any standard preconditioner. We give a detailed analysis on this new preconditioning idea and show how the number of iterations for the inner iterative method and hence the total number of iterations can be reduced significantly by the application of this tuning strategy. The analysis of the tuned preconditioner is carried out for both Hermitian and non-Hermitian eigenproblems. We show how the preconditioner can be implemented efficiently and illustrate its performance using various numerical examples. An equivalence result between the preconditioned simplified Jacobi-Davidson method and inexact inverse iteration with the tuned preconditioner is given. Finally, we discuss the shift-invert Arnoldi method both in the standard and restarted fashion. First, existing relaxation strategies for the outer iterative solves are extended to implicitly restarted Arnoldi's method. Second, we apply the idea of tuning the preconditioner to the inner iterative solve. As for inexact inverse iteration the tuned preconditioner for inexact Arnoldi's method is shown to provide significant savings in the number of inner solves. The theory in this thesis is supported by many numerical examples.
DIGITAL SIMULATION OF NON-GAUSSIAN STATIONARY PROCESSES USING KARHUNEN-LOEVE EXPANSION

A new simulation algorithm is developed for generating non-Gaussian processes with a specified marginal distribution function and covariance function. It utilizes the Karhunen-Loeve (K-L) expansion for simulation and an iterative mapping scheme to fit the target marginal distribution function. A stationary random process with Gamma marginal distribution is used to demonstrate the validity and convergence characteristics of the proposed algorithm.