Miracle-dz/UniFAR-FTUs huggingface dataset:
Subgoal- and Goal-Related Prediction Errors in Medial Prefrontal Cortex

A longstanding view of the organization of human and animal behavior holds that behavior is hierarchically organized, meaning that it can be understood as directed towards achieving superordinate goals through subordinate goals, or subgoals. For example, the superordinate goal of making coffee can be broken down as accomplishing a series of subgoals, namely boiling water, grinding coffee, pouring cream, etc. Learning and behavioral adaptation depend on prediction-error signals, which have been observed in ventral striatum (VS) and medial prefrontal cortex (mPFC). In past work, we have shown that prediction error signals (PEs) can be linked not only to superordinate goals, but also to subgoals. Here we present two functional magnetic resonance imagining experiments that replicate and extend these findings. In the first experiment, we replicated the finding that mPFC signals subgoal-related PEs, independently of goal PEs. Together with our past work, this experiment reveals that BOLD responses to PEs in mPFC are unsigned. In the second experiment, we showed that when a task involves both goal and subgoal PEs, mPFC shows only goal-related PEs, suggesting that context or attention can strongly impact hierarchical PE coding. Furthermore, we observed a dissociation between the coding of PEs in mPFC and VS. These experiments suggest that the mPFC selectively attends to information at different levels of hierarchy depending on the task context.
Modeling the Past and Current Distribution and Habitat Suitability for Two Snake-eyed Skinks, Ablepharus grayanus and A. pannonicus (Sauria: Scincidae)

The study of the climate variability in the past and present, correlating those with changes in the distribution range of species, has attracted considerable research interest. The genus Ablepharus consists of 10 recognized species, of which A. bivittatus , A. grayanus , and A. pannonicus are documented from Iran. In the present study, we modeled with MaxEnt the potential distribution areas and determined the suitable habitats in the past [mid-Holocene (MH) and the last interglacial (LIG)] and their current distribution for two species of snake-eyed skinks ( A. grayanus and A. pannonicus ) separately. Models of the species indicated good fit by the average high area under the curve (AUC) values ( A. grayanus = 0.929 ± 0.087 and A. pannonicus = 0.979 ± 0.007). Precipitation of the driest quarter of the year, mean temperature of the coldest quarter of the year, and precipitation of the driest month variables made important contributions to A. grayanus . Two important climate variables contributed importantly to A. pannonicus : temperature seasonality and mean temperature of the wettest quarter of the year and one topographic variable, slope. We conclude that these variables form a natural barrier for species dispersal. The MH and the LIG models indicated a larger suitable area than the current distribution.
Linearization Methods in Time Series Analysis

In this dissertation, we propose a set of computationally efficient methods based on approximating/representing nonlinear processes by linear ones, so-called linearization. Firstly, a linearization method is introduced for estimating the multiple frequencies in sinusoidal processes. It utilizes a regularized autoregressive (AR) approximation, which can be regarded as a “large p small n” approach in a time series context. An appealing property of regularized AR is that it avoids a model selection step and allows for an efficient updating of the frequency estimates whenever new observations are obtained. The theoretical analysis shows that the regularized AR frequency estimates are consistent and asymptotically normally distributed. Secondly, a sieve bootstrap scheme is proposed using the linear representation of generalized autoregressive conditional heteroscedastic (GARCH) models to construct prediction intervals (PIs) for the returns and volatilities. Our method is simple, fast and distribution-free, while providing sharp and wellcalibrated PIs. A similar linear bootstrap scheme can also be used for diagnostic testing. Thirdly, we introduce a robust lagrange multiplier (LM) test, which utilizes either the bootstrap or permutation procedure to obtain critical values, for detecting GARCH effects. We justify that both bootstrap and permutation LM tests are consistent. Intensive numerical studies indicate that the proposed resampling algorithms significantly improve the size and power of the LM test in both skewed and heavy-tailed processes. Moreover, fourthly, we introduce a nonparametric trend test in the presence of GARCH effects (NT-GARCH) based on heteroscedastic ANOVA. Our empirical evidence show that NT-GARCH can effectively detect non-monotonic trends under GARCH, especially in the presence of irregular seasonal components. We suggest to apply the bootstrap procedure for both selecting the window length and finding critical values. The newly proposed methods are illustrated by applications to astronomical data, to foreign currency exchange rates
Antibiotic Susceptibility Pattern of Enterobacteriaceae Isolated from Raw Meat and Ghanaian Coin Currencies at Cape Coast Metropolis, Ghana: The Public Health Implication

The emergence and upsurge of Multiple Antibiotic Resistant (MDR) Enterobacteriaceae in the environment is a cause of concern as this can result in an outbreak and spread to healthcare settings. MDR Enterobacteriaceae have been associated with high morbidity and mortality due to delay in selecting and delivering active therapy in time. The study was conducted to investigate the level of contamination of raw meat and Ghanaian coins in circulation at Cape Coast Metropolis. In all, 10 raw meat were sampled each from chevron and beef from Kotokuraba market, and 400 Ghanaian coin currencies retrieved from food vendors, students, transport operators and banks were used in this study. The Enterobacteriaceae species isolated were tested for their susceptibility to Ampicillin, Tetracycline (TET), Gentamicin (GEN), Cotrimoxazole (COT), Cefuroxime (CRX), Cefixime (CXM), Cefotaxime (CTX), Penicillin (PEN), Cloxacillin (CXC), Erythromycin (ERY) and Amikacin (AMK) antibiotics using Mueller-Hinton agar antibiotic diffusion technique. Of the isolated Enterobacteriaceae, 30% and 62% from chevron and beef respectively and 14.17%, 13.75% and 10.63% from food vendors, students and transport operators respectively showed resistance to some of the antibiotics tested. 8.6% of the Escherichia coli (E. coli) isolated from chevon were resistant to CRXr-CHLr-AMPr-COTr-GEMr and 15.5% of CRXi-CHLi-AMPr-TETr-COTr from beef. 40.0% of E. coli isolated from coin currencies were resistant to CRXr-CHLr-AMPr-TETr-CTXr, 50.0% of Enterobacter spp to CRXr-CHLr-AMPr-TETr-CTXr, 16.67% of Proteus spp to CRXi-CHLi-AMPr-TETr-AMKi, 40% Pseudomonas spp to CRXr-AMPr-TETr-AMKi and 100% of Enterobacter spp to CRXr-AMPr-TETi-CTXr. The multidrug-resistant Enterobacteriaceae isolates from circulating Ghanaian coins and raw meats in the Cape Coast metropolis is an indication of an impending danger which requires immediate attention to prevent a possible outbreak and spread from the society to the hospital setting.
STAT3 Genotypic Variant rs744166 and Increased Tyrosine Phosphorylation of STAT3 in IL-23 Responsive Innate Lymphoid Cells during Pathogenesis of Crohn's Disease

Crohn's disease (CD) results from dysregulated immune responses to gut microbiota in genetically susceptible individuals, affecting multiple areas of the gastrointestinal tract. Innate lymphoid cells (ILCs) are tissue-resident innate effector lymphocytes which play crucial roles in mucosal immune defense, tissue repair, and maintenance of homeostasis. The accumulation of IFN-γ-producing ILC1s and increased level of proinflammatory cytokines produced by ILCs has been observed in the inflamed terminal ileum of CD patients. To date, the precise mechanisms of ILC plasticity and gene regulatory pathways in ILCs remain unclear. Signal transducer and activator of transcription 3 (STAT3) regulates gene expression in a cell-specific, cytokine-dependent manner, involving multiple immune responses. This study proposes the positive correlation between the prevalence of STAT3 rs744166 risky allele “A” with the severity of disease in a cohort of 94 CD patients. In addition, the results suggest an increased STAT3 activity in the inflamed ileum of CD patients, compared to unaffected ileum sections. Notably, IL-23 triggers the differentiation of CD117+NKp44− ILC3s and induces the activation of STAT3 in both CD117+NKp44− and CD117−NKp44− ILC subsets, implying the involvement of STAT3 in the initiation of ILC plasticity. Moreover, carriage of STAT3 “A” risk allele exhibited a higher basal level of STAT3 tyrosine phosphorylation, and an increased IL-23 triggered the pSTAT3 level. We also demonstrated that there was no delayed dephosphorylation of STAT3 in ILCs of both A/A and G/G donors. Overall, the results of this study suggest that IL-23-induced activation of STAT3 in the CD117−NKp44− ILC1s involves in ILC1-to-ILC3 plasticity and a potential regulatory role of ILC1 function. Those genetically susceptible individuals carried STAT3 rs744166 risky allele appear to have higher basal and cytokine-stimulated activation of STAT3 signal, leading to prolonged inflammation and chronic relapse.
Implications for Integrating the Interactive Whiteboard and Professional Development to Expand Mathematics Teachers TPACK in an Urban Middle School

Implications for Integrating the Interactive Whiteboard and Professional Development to Expand Mathematics Teachers TPACK in an Urban Middle School. (August 2011) Jamaal Rashad Young, B.S. Texas A&M University; M.Ed., Texas A&M University Chair of Advisory Committee: Dr. Robert M. Capraro The Federal Government is dedicated to improving student achievement through technology. This dedication is most apparent in the area of federal spending. One explanation for the lack of results in student achievement is that teachers need appropriate training to effectively teach with technology. This study integrates the interactive whiteboard and professional development in order to develop middle school mathematics teachers’ Technological Pedagogical Content knowledge (TPACK) in an urban school. Teacher TPACK is measured on a modified version of Survey of Teacher Knowledge to Teach with Technology. Student achievement is measured on the Texas Assessment of Knowledge and Skills (TAKS), a standardized mathematics assessment. Teachers in this study receive three weeks of professional development during their team planning periods to help them integrate the Interactive Whiteboard (IWB) into their mathematics instruction. Mean difference effect sizes are used to measure teacher gain in TPACK. Student achievement scores before and after the professional development are analyzed by Multi-way ANOVA after propensity scores are used to match participant students to a separate group of control students for comparison.
Effect of different dietary protein sources on hematological parameters of striped catfish Pangasianodon hypophthalmus

The present study was conducted with the aim to evaluate performance of different protein source on growth, survival and hematological parameters in striped catfish P. hypophthalmus. The experiment was conducted at College of Fisheries, Guru Angad Dev Veterinary and Animal Sciences University, Ludhiana, Punjab, during JulyOctober, 2017 for a duration of 120 days in indoor glass aquaria (60× 30 ×30cm) maintaining stocking density of 8 no of P. hypophthalmus fingerling (9.80±0.08 cm and 11.0±0.06 g) in each aquaria. Four iso-proteinous (≈ 32% crude protein) experimental diets (D1 – D4) were prepared containing poultry waste (D1), fish meal (D2), fish silage (D3) and soybean (D4) as major protein source in diets in four treatments T1T4, respectively. No significant differences were observed in water quality parameters among different treatments fed with different sources of protein. Maximum net weight gain was recorded in T4 (19.329 g) followed by T2 (16.154 g), T3 (14.583 g) and T1 (11.937 g), respectively indicating diet containing soybean meal as major protein source gained highest weight in P. hypophthalmus. Hemoglobin value ranged 5.8-7.1g dL while erythrocyte count 1.44-2.75 mill cu.mm, PCV 16.4-33.4%, MCV 113.9-123.0 fL, MCH 24.7-32.6 pg, MCHC 20.6-28.7 g dL recorded in fish blood. Among leukocytes, range of count for neutrophils 60.2-84.7%, lymphocytes 8.2-25.5%, monocytes 0.8-4.0% and eosinophils 0.0 – 22.3% recorded in fish blood, fed with different diets. P. hypophthalmus appeared to exhibit a better response towards survival, growth and acquired immunity of fish when fed with soybean rich diet as compared to fish silage, poultry slaughter waste and fish meal.
Molecular identification and characterization of phytoplasmas associated with carrot, cabbage and onion crops and their insect vectors in Punjab, Pakistan.

Phytoplasmas are bacterial plant pathogens and obligate parasites lacking cell walls. They are phloem-limited, uncultivable mostly causing diseases in numerous plants worldwide (Lee et al., 2000; IRPCM, 2004). Globally, phytoplasmas cause multiple diseases in several crop species including vegetables, fruits, cereals (Lee et al., 2000). Different crops have been reported to be infected by many viruses, bacteria and fungal diseases but in addition nested PCR studies using particular phytoplasma primers (P1/P7 and R16F2n/R16R2) specified phytoplasma incidence in symptomatic plants (Ahmad et al., 2015). A varied of symptoms induced due to phytoplasma infection including leaf yellowing, little leaf, virescence, growth aberrations (proliferation, dwarfism), and more commonly flower abnormalities and alteration of gene expression are faced (McCoy et al., 1989; Del Serrone et al., 2001; Ahmad et al., 2013). Phytoplasma is also reported to change the plant physiology as DNA methylation was studied as a potential mechanism for ruling floral gene expression in tomato buds infected with stolbur phytoplasma (Ahmad et al., 2013). In year 2007, phytoplasmas connected with various subgroups of the AY phytoplasma group (16SrI) were spotted to be linked with low prevalence of infections in carrots presenting leaves redness, qualitative reduction of tap roots and shoot proliferation (Duduk et al., 2007). Phytoplasmas are transferred among plants by phloem sap-sucking insect vectors of different families including Psyllidae, Cicadellidae, and Cixidae, in which they reproduce (Lee and Davis, 1992). Transovarial transmission of some phytoplasmas in insects has also been reported (Danielli et al., 1996; Alma et al., 1997; Mitsuhashi et al., 2002). Transmission of phytoplasmas can also be conceded through grafting and vegetative propagation including cutting, storage tubers, rhizomes or bulbs (Lee and Davis, 1992). Different dodder species (Cuscuta campestres, epilinum and trifolli), the plant parasites, affecting various plants including tomatoes are also responsible for the transmission of phytoplasmas (Salehi et al., 2014). So far, various phytoplasma strains have been categorized into 28 groups using PCR with universal primers and RFLP examination Pak. J. Agri. Sci., Vol. 56(2),407-414; 2019 ISSN (Print) 0552-9034, ISSN (Online) 2076-0906 DOI:10.21162/PAKJAS/19.7152. http://www.pakjas. com.pk
Asymptotic Behavior of Near Critical Branching Processes and Modeling of Cell Growth Data

DOMINIK REINHOLD: Asymptotic Behavior of Near Critical Branching Processes and Modeling of Cell Growth Data. (Under the direction of Amarjit Budhiraja and M. Ross Leadbetter.) This dissertation is composed of two parts, a theoretical part, in which certain asymptotic properties of near critical branching processes are studied, and an applied part, consisting of statistical analysis of cell growth data. First, near critical single type Bienaymé-Galton-Watson (BGW) processes are considered. It is shown that, under appropriate conditions, Yaglom distributions of suitably scaled BGW processes converge to that of the corresponding diffusion approximation. Convergences of stationary distributions for Q-processes and models with immigration to the corresponding distributions of the associated diffusion approximations are established as well. Moreover, convergence of Yaglom distributions of suitably scaled multitype subcritical BGW processes to that of the associated diffusion model is established. Next, near critical catalyst-reactant branching processes with controlled immigration are considered. The catalyst population evolves according to a classical continuous time branching process, while the reactant population evolves according to a branching process whose branching rate is proportional to the total mass of the catalyst. Immigration takes place exactly when the catalyst population falls below a certain threshold, in which case the population is instantaneously replenished to the threshold. A diffusion limit theorem for the scaled processes is established, in which the catalyst limit is a reflected diffusion and the reactant limit is a diffusion with coefficients depending on the reactant. Stochastic averaging under fast catalyst dynamics are considered next. In the setting where both catalyst and reactant evolve according to the above described (reflected)
No Association of Prolactin Receptor (PRLR) Gene and litter size in Gaddi Goat Breed Reared under Migratory System in Western Himalayan Ranges of Himachal Pradesh

Gaddi is the predominant Indian goat breed also known as “White Himalayan goat”, constituting 60-65% of total goats in the state of Himachal Pradesh. The polymorphism of prolactin receptor (PRLR) gene was found to have relationship with prolificacy in goats. In present study, polymorphism of intron 2 region of PRLR gene was investigated in Gaddi goats (n = 89) using PCR-SSCP and DNA sequencing approach. PCR-SSCP assay of 176 bp amplicon of intron 2 region of PRLR gene revealed polymorphism with three types of genotypes viz., AA, AB and BB with genotypic frequencies as 0.31, 0.55 and 0.14, respectively. The allelic frequency of alleles A and B were 0.59 and 0.41, respectively in all the screened goat population. Genetic diversity analysis revealed the value of Ne, Hobs, Hexp and PIC were 1.96, 0.52, 0.49 and 0.37, respectively. The Ne and Hobs values also indicated that sufficient genetic variation exists at the studied locus. FIS estimate was observed as -0.15 indicating heterozygous excess at studied locus. DNA sequencing of amplified product revealed one nucleotide mutation (T92C) in intron 2 region of PRLR gene. The mean litter size in AA, AB and AB genotypes were 1.27±0.12, 1.41±0.09 and 1.84±0.26, respectively. No significant (P>0.05) associations of PRLR genotypes with litter size were observed. Effect of season and parity were also found to be non-significant (P>0.05) on litter size. Consequently, the study on additional data based on more number of animals in diversified flock should be carried out for future association studies.
Yield responses to elevated CO2 concentration among Japanese rice cultivars released since 1882

ABSTRACT Atmospheric CO2 concentrations ([CO2]) have increased by more than 100 μmol mol−1 over the last century and are projected to rise further. Breeding cultivars with a greater response to elevated [CO2] (E-[CO2]) can be an effective adaptation to global climate change. We wondered whether E-[CO2]-responsive cultivars have been unintentionally selected through empirical breeding as [CO2] has increased. If so, modern cultivars may respond better to E-[CO2] than old ones. We conducted free-air CO2 enrichment (FACE) experiments in 2 years to examine whether rice cultivars bred in different eras differ in response to E-[CO2] and to determine any associated traits. We tested five Japanese cultivars: Aikoku (released in 1882), Norin 8 (1934), Koshihikari (1956), Akihikari (1976) and Akidawara (2009). The yields of Aikoku and Norin 8 increased by 19.3% and 30.3%, respectively, under E-[CO2], while those of Koshihikari and Akihikari increased by 15.9% and 3.4%, respectively. However, that of Akidawara, the newest cultivar, also increased by 19.0%. Norin 8’s strong response to E-[CO2] was associated with increases in both spikelet density and percentage of ripened grains, both of which were closely related to nitrogen uptake. These results suggest that breeding has not necessarily improved cultivars’ response to E-[CO2], and that selection for traits such as sink capacity and nitrogen uptake can be effective to improve rice productivity under E-[CO2]. Graphical Abstract
Mathematics, gender, and large scale data: new directions or more of the same?

It is now frequently argued that intervention programs aimed at improving schooling for females have been so successful that males, as a group, should be perceived as disadvantaged: in terms of educational participation, adjustment to schooling, and achievement in most subjects including mathematics. In this paper we examine two large data bases for possible gender differences: the Australian Mathematics Competition [AMC] – for which participation is voluntary and the mathematics course in the Victorian Certificate of Education [VCE] most frequently used as a prerequisite for entry into many tertiary courses. Greater male participation was found for both tests. Gender differences at the high performance levels also favoured males, but were more marked for the AMC.
Resolving complexity of within-host pathogen strain diversity and antimicrobial resistance using optimization and machine learning

Hosts such as humans and arthropods are often infected by diverse bacterial populations and such heterogeneity poses a great threat in effective treatments. Moreover, the development of antimicrobial resistance further aggravates the efficacy of treatment. In this thesis, we present work towards solving two crucial problems in the realm of epidemiology, the withinhost strain diversity problem and the antimicrobial resistance problem. For the strain diversity problem, we resolved complex infections and co-infections pattern within a sample by developing a two-stage optimization pipeline using integer linear programming. Results on simulated data showed that our methods achieved a precision of at least 92% and a recall of at least 90% for the first-stage of our pipeline, and a soft-precision of at least 68% and a soft-recall of at least 79% for the second-stage. Soft-precision and soft-recall are similar to precision and recall but less stringent. This demonstrates that our methods are able to predict strains which are extremely close to the true strains and are comparable to or better than existing tools. For the antimicrobial resistance problem, we explored different machine learning models to classify the response of a pathogen to a single drug, where we specifically focused on analyzing the robustness of the models and deriving resistance-related markers from them. The models achieved at least 85% test AUC (Area under the ROC curve) for first-line drugs and at least 76% for second-line drugs. Our results showed that the models are robust given datasets of varying diversity, and the resistance-related markers which were frequently reported in the literature were highly ranked by the models. Our work on both problems paves the way for robust strain typing in the presence of withinhost heterogeneity and effective drug resistance diagnosis, overcoming essential challenges to solving both problems which are currently not addressed by any existing methodology for pathogen genomics.