Miracle-dz/UniFAR-FTUs huggingface dataset:
Next Generation of Genotype Imputation Methods

In the past several years, we have witnessed numerous human genetic studies that have systematically evaluated the contribution of genetic polymorphisms to various complex diseases, and enabled the evolution of multiple treatment strategies, particularly pharmaceutical therapies. Genotype imputation has been a key step in such studies increasing the power of gene mapping analyses, facilitating harmonization of results across studies, and accelerating fine-mapping efforts. Imputation requires access to a reference panel of densely sequenced genomes and is a computationally intensive process, even with modern high performance computing. Furthermore, reference panels often have data privacy issues that inhibit users from having direct access to the data. The goal of this dissertation is to design novel strategies to address these challenges for the next generation of imputation methods. In the first project, I describe our efforts to create a reference panel of ~32, 000 individuals with ~40M variants by combining genetic information obtained across 20 whole genome sequencing studies (Haplotype Reference Consortium). In the second project, I describe a novel idea called ‘state space reduction’ that reduces computational requirements of genotype imputation by orders of magnitude without any loss of accuracy (minimac3). I also present a web-based platform for imputation that greatly improves user experience and productivity. In the third project, I extend the idea of state space reduction by implementing a more complex version of the strategy that produces additional cost savings (minimac4). In the fourth project, I introduce the idea of meta-imputation: a novel approach that integrates imputed data from multiple reference panels at overlapping sites without interfering in the imputation algorithm (MetaMinimac). In summary, the purpose of this dissertation research is to develop statistical methods and com-
Productivity, setup time and costs of a winch-assisted forwarder

ABSTRACT In fully mechanized cut-to-length timber harvesting operations, the forwarder represents the limiting machine on steeper terrain in terms of trafficability. In order to operate also on steep terrain and on soft soils with low traction they can be equipped with traction winches. The objective of this study was to investigate setup time, develop a productivity model and calculate extraction costs for the winch-assisted forwarder John Deere 1110E. The productivity model is based on 75 observed cycles within 18 skid trails. The study was carried out in three different stands using detailed productivity and process analyses. Factors, which influence machine productivity, are piece volume (pv), inclination, distance during loading activities and extraction distance. With an average observed pv of 0.10 m3 and an average load volume of 9.25 m3, the winch-assisted forwarder reached a productivity of 13.7 m3/PSH15, according to the developed model. By an annual utilization of 1,900 h and system costs for the entire machinery of 110.68 €/PSH15, forwarding costs 8.06 €/m3. The detailed time and motion study showed different possibilities for mounting the cable depending on operation direction, terrain, passability through the stand and availability of the harvester. Average setup time for the cable operating downhill was 21.6 min, which additionally caused costs of 1.03 €/m3.
Yield and Soluble Solids Content of Winter-grown Spinach in Unheated High Tunnels in New England

Fall planting of spinach ( Spinacia oleracea L.) into high tunnels for harvest from late fall through early spring is widely practiced in the northeastern United States, but replicated studies focusing on this production system are lacking. The objectives of our study were to understand the effect of fall planting date (PD) and cultivar on yield and soluble solids content (SSC) of spinach. Three cultivars (Regiment, Space, and Tyee) were transplanted in unheated high tunnels in Durham, NH, in 2014–15 (Year 1) and 2015–16 (Year 2) at six different fall dates: 20 Sept. , 30 Sept. , 9 Oct., 19 Oct., 30 Oct., and 9 Nov. Five additional cultivars (Carmel, Corvair, Gazelle, Emperor, and Renegade) were included at the third date (9 Oct.) to compare yield and SSC among cultivars during winter months. A randomized complete block design with four replications was used for all experiments. Year and fall transplant date had a signiﬁcant effect on total yield. Total yield of Year 2 was nearly double that of Year 1 for all PDs and cultivars. In both years, total yield decreased with later planting, such that yield from the 20 Sept. date was greater than a minimum of three of ﬁve subsequent PDs, depending on year. Total yield in spring (January through April) did not differ among the ﬁrst four PDs in Year 1 or among any dates in Year 2, suggesting that a wide range of PDs will work well for those primarily interested in spring Combined analyses of the data from both showed no signiﬁcant differences in total yield among the eight cultivars planted only on 9 Oct. of the three cultivars grown at all PDs, Regiment produced signiﬁcantly higher yields than Tyee. Harvest date, cultivar, and harvest date 3 cultivar affected leaf and petiole sap SSC in both years. SSC was most strongly negatively correlated with air and soil temperatures at a 10-day interval in Year 1 ( R 2 = 0.61 and 0.64, respectively) and a 7-day interval in Year 2 ( R 2 = 0.78 and 0.69, respectively). ‘Gazelle’ and ‘Emperor’ contained among the highest SSC in both years. Our work demonstrates total yield is highly dependent on fall PD and the growing conditions of a given year.
Immunological studies of trypanosoma evansi infections in rabbits

CHAPTER ONE LITERATURE REVIEW CHAPTER TWO OPTIMIZATION OF IMMUNOBLOTTING TECHNIQUE FOR THE DETECTION OF ANTIGENIC COMPONENTS OF TRYPANOSOMA EVANSI CHAPTER THREE CHARACTERISATION OF THE SURFACE COAT OF TRYPANOSOMA EVANSI AND THE CLASS-SPECIFIC ANTIBODY RESPONSE TO IT IN RABBITS EXPERIMENTALLY INFECTED WITH TRYPANOSOMA EVANSI CHAPTER FOUR CLASS-SPECIFIC ANTIBODY RESPONSE IN RABBITS EXPERIMENTALLY INFECTED WITH T. EVANSI DURING THE PERIOD OF PRIMARY INFECTION AND AFTER DRUG TREATMENT CHAPTER FIVE CLASS-SPECIFIC ANTIBODY RESPONSE IN RABBITS AFTER REINFECTION WITH TRYPANOSOME SPECIES
Compensatory growth after feed restriction during the rearing period in pigs

The compensatory growth after feed restriction was studied in an experiment with 120 pigs which were divided into two test treatments: control (C) and restricted (R) feeding. During the first period, from the age of seven weeks to 25 kg of live weight, R pigs were fed twice and C pigs three times the maintenance level. During the second period, from 25 kg to 100 kg of live weight, both treatments were given the same amount of feed from 1.4 to 3.2 feed units/pig/day. The daily feed intake of R pigs was significantly lower (p<0.001) than that of C pigs during the restriction period (0.69 vs. 0.99 FU/pig/d). R pigs gained also significantly less weight (p<0.01) than C pigs (344 vs. 527 g/d) and the length of the first period was longer for R pigs compared to C pigs (p<0.001). During the second period R pigs compensated the retarded growth caused by feed restriction. R pigs gained significantly more weight (p<0.01) than C pig (955 vs. 924 g/d) and feed conversion efficiency (FCE) was better (2.52 vs. 2.60 FU/kg gain) (p<0.05). Significant differences were found also between the treatments in the length of the second period (p<0.05) and in the total feed consumption (p<0.05). No differences were found in carcass composition between the treatments. Fullsib test indexes were calculated from the results of the second period for both treatments based on the method used in Finnish on-station progeny testings. The index means forC and R pigs were 2.7 and 6.3, respectively.
Combined Influence of Bud Load and Micronutrients on Physico-chemical Traits of Grape cv. Sahebi

This work was carried out in collaboration between all authors. Author AK performed the study, carried out the statistical analysis of the study and wrote the first draft of the manuscript. Authors NN, MKS, RB, KJ and SA designed and monitored the study and managed the analysis of the study. Author AK managed the literature searches. All authors read and approved the final manuscript. ABSTRACT The study on the combined influence of bud load and micronutrients on physicochemical traits of grape cv. Sahebi was carried out in model grapevine orchard of the Department of Horticulture at Kralbagh, Tehsil Lar Distt. Ganderbal (J&K) for two consecutive years to standardise the bud load and micronutrients application for improving physic-chemical traits in grape cv. Sahebi. The experiment consisted of 15 treatments with 3 levels of budload B 1 (96 buds/vine), B 2 (128 buds/ vine) and B 3 (160 buds/vine), 3 levels of micronutrients viz. M 1 (Solubor 0.1%), M 2 (ZnSO 4 0.4%) and M 3 (Solubor 0.1% + ZnSO 4 0.4%) applied two weeks before bloom and their 9 combinations (B 1 M 1 , B 1 M 2, B 1 M 3, B 2 M 1, B 2 M 2, B 2 M 3, B 3 M 1, , B 3 M 2 , , B 3 M 3 ) replicated thrice with a double plot size in a completely randomized block design. Among the different treatments budload B 2 (128 buds/vine) recorded maximum fruitful shoots, bunch length, berry length, total soluble solids /acid ratio and minimum shot berry percentage Maximum fruitful shoots, number of bunches, bunch diameter, berry length, berry diameter, total soluble solids/acid ratio, ascorbic acid and shot berry percentage was observed in micronutrient M 1 (Solubar-0.1%). The combination of B 2 M 1 observed highest fruitful shoots, berry length, total soluble solids /acid ratio, ascorbic acid, and lowest shot berry percentage. Thus it was concluded that budload B 2 (128 buds/vine), M 1 (Solubor 0.1%) and their combination B 2 M 1 proved to be the best for improving physico–chemical traits of grape cv. Sahebi.
Variational Adversarial Active Learning

Active learning aims to develop label-efficient algorithms by sampling the most representative queries to be labeled by an oracle. We describe a pool-based semi-supervised active learning algorithm that implicitly learns this sampling mechanism in an adversarial manner. Our method learns a latent space using a variational autoencoder (VAE) and an adversarial network trained to discriminate between unlabeled and labeled data. The mini-max game between the VAE and the adversarial network is played such that while the VAE tries to trick the adversarial network into predicting that all data points are from the labeled pool, the adversarial network learns how to discriminate between dissimilarities in the latent space. We extensively evaluate our method on various image classification and semantic segmentation benchmark datasets and establish a new state of the art on CIFAR10/100, Caltech-256, ImageNet, Cityscapes, and BDD100K. Our results demonstrate that our adversarial approach learns an effective low dimensional latent space in large-scale settings and provides for a computationally efficient sampling method. Our code is available at \url{https://github.com/sinhasam/vaal}.
Solution structure of discrete integrable systems associated with $\mathbb{Z}_\mathcal{N}$ graded Lax pairs

Fordy and Xenitidis [J. Phys. A: Math. Theor. 50 (2017) 165205] recently proposed a large class of discrete integrable systems which include a number of novel integrable difference equations, from the perspective of $\mathbb{Z}_\mathcal{N}$ graded Lax pairs, without providing solutions. In this paper, we establish the link between the Fordy-Xenitidis discrete systems in coprime case and linear integral equations in certain form, which reveals solution structure of these equations. The bilinear form of the Fordy-Xenitidis integrable difference equations is also presented together with the associated general tau function. Furthermore, the solution structure explains the connections between the Fordy-Xenitidis novel models and the discrete Gel'fand-Dikii hierarchy.
Natural Deduction Assistant (NaDeA)

We present the Natural Deduction Assistant (NaDeA) and discuss its advantages and disadvantages as a tool for teaching logic. NaDeA is available online and is based on a formalization of natural deduction in the Isabelle proof assistant. We first provide concise formulations of the main formalization results. We then elaborate on the prerequisites for NaDeA, in particular we describe a formalization in Isabelle of "Hilbert's Axioms" that we use as a starting point in our bachelor course on mathematical logic. We discuss a recent evaluation of NaDeA and also give an overview of the exercises in NaDeA.
Certifying Polynomial Nonnegativity via Hyperbolic Optimization

We describe a new approach to certifying the global nonnegativity of multivariate polynomials by solving hyperbolic optimization problems---a class of convex optimization problems that generalize semidefinite programs. We show how to produce families of nonnegative polynomials (which we call hyperbolic certificates of nonnegativity) from any hyperbolic polynomial. We investigate the pairs $(n,d)$ for which there is a hyperbolic polynomial of degree $d$ in $n$ variables such that an associated hyperbolic certificate of nonnegativity is not a sum of squares. If $d\geq 4$ we show that this occurs whenever $n\geq 4$. In the degree three case, we find an explicit hyperbolic cubic in $43$ variables that gives hyperbolic certificates that are not sums of squares. As a corollary, we obtain the first known hyperbolic cubic no power of which has a definite determinantal representation. Our approach also allows us to show that, given a cubic $p$, and a direction $e$, the decision problem "Is $p$ hyperbolic with respect to $e$? " is co-NP hard.
ISOLASI DAN IDENTIFIKASI BAKTERI Vibrio sp. PADA KERANG KAPAH (Meretrix meretrix) DI KABUPATEN TRENGGALEK

Meretrix meretrix is one type of shellfish that are included in the bivalves that are filter feeders that live in the waters. Many bacteria that live in the estuary with high salinity in the range of 20-40 ppt one of which is the Vibrio bacterium. This research aims to determine the presence of Vibrio spp . bacteria in M. meretrix from Cengkrong Mangrove Eduwisata River, Trenggalek. The Isolation of Vibrio bacteria was conducted by streat plate method on selective media of TCBSA (Thiosulfate Citrate Bile Salt Sucrose Agar) and identify the Vibrio bacterium through the morphological and biochemical tests based Bergey's Manual of Systematic Bacteriology In Microbiology laboratory of Biology Faculty of Gadjah Mada University. The Result showed there are 7 isolates Vibrio spp. bacterias in M. meretrix they are isolate 1.1, 1.4, 1.7, 1.8. 5.3, 3.5, 2.6 PSBI Keyword: Meretrix meretrix, Vibrio, identification
Temperature effects on the electronic band structure of PbTe from first principles

We report a fully {\it ab-initio} calculation of the temperature dependence of the electronic band structure of PbTe. We address two main features relevant for the thermoelectric figure of merit: the temperature variations of the direct gap and the difference in energies of the two topmost valence band maxima located at L and $\Sigma$. We account for the energy shift of the electronic states due to thermal expansion, as well as electron-phonon interaction computed using the non-adiabatic Allen-Heine-Cardona formalism within density functional perturbation theory and the local density approximation. We capture the increase of the direct gap with temperature in very good agreement with experiment. We also predict that the valence band maxima at L and $\Sigma$ become aligned at $\sim 600-700$ K. We find that both thermal expansion and electron-phonon interaction have a considerable effect on these temperature variations. The Fan-Migdal and Debye-Waller terms are of almost equal magnitude but have an opposite sign, and the delicate balance of these terms gives the correct band shifts. The electron-phonon induced renormalization of the direct gap is produced mostly by high-frequency optical phonons, while acoustic phonons are also responsible for the alignment of the valence band maxima at L and $\Sigma$.
Wavenumber Explicit Analysis for Galerkin Discretizations of Lossy Helmholtz Problems

We present a stability and convergence theory for the lossy Helmholtz equation and its Galerkin discretization. The boundary conditions are of Robin type. All estimates are explicit with respect to the real and imaginary part of the complex wave number $\zeta\in\mathbb{C}$, $\operatorname{Re}\zeta\geq0$, $\left\vert \zeta\right\vert \geq1$. For the extreme cases $\zeta \in\operatorname*{i}\mathbb{R}$ and $\zeta\in\mathbb{R}_{\geq0}$, the estimates coincide with the existing estimates in the literature and exhibit a seamless transition between these cases in the right complex half plane.
Crepant resolution and the holomorphic anomaly equation for [C3/Z3]

We study the orbifold Gromov–Witten theory of the quotient [C3/Z3] in all genera. Our first result is a proof of the holomorphic anomaly equations in the precise form predicted by B ‐model physics. Our second result is an exact crepant resolution correspondence relating the Gromov–Witten theories of [C3/Z3] and local P2 . The proof of the correspondence requires an identity proven in the Appendix by T. Coates and H. Iritani.
Understanding Neural Architecture Search Techniques

Automatic methods for generating state-of-the-art neural network architectures without human experts have generated significant attention recently. This is because of the potential to remove human experts from the design loop which can reduce costs and decrease time to model deployment. Neural architecture search (NAS) techniques have improved significantly in their computational efficiency since the original NAS was proposed. This reduction in computation is enabled via weight sharing such as in Efficient Neural Architecture Search (ENAS). However, recently a body of work confirms our discovery that ENAS does not do significantly better than random search with weight sharing, contradicting the initial claims of the authors. We provide an explanation for this phenomenon by investigating the interpretability of the ENAS controller's hidden state. We find models sampled from identical controller hidden states have no correlation with various graph similarity metrics, so no notion of structural similarity is learned. This failure mode implies the RNN controller does not condition on past architecture choices. Lastly, we propose a solution to this failure mode by forcing the controller's hidden state to encode pasts decisions by training it with a memory buffer of previously sampled architectures. Doing this improves hidden state interpretability by increasing the correlation between controller hidden states and graph similarity metrics.
Évolution génotypique et phénotypique d'une souche épidémique de Pseudomonas aeruginosa au cours des 11 ans de sa diffusion hospitalière

P. aeruginosa est une bacterie pathogene de l'homme, responsable d'infections nosocomiales chez les patients immunodeprimes. Bien que son evolution au sein d'un patient soit bien decrite, son evolution genomique globale au cours de sa propagation dans un hopital est tres mal connue. Le clone a haut-risque ST395 multiresistant aux antibiotiques a diffuse dans le Centre Hospitalier Regional Universitaire de Besancon entre 1997 et 2008 en infectant ou colonisant plus de 300 patients. Une approche WGS a ete utilisee afin d'identifier l'origine de l'epidemie, les caracteristiques ayant aide a son installation a l'hopital ainsi que celles a l'origine de sa disparition. Les genomes de 54 isolats representatifs de l'epidemie ont ete sequences. L’arbre phylogenetique a mis en evidence deux clusters distincts indiquant la presence de deux epidemies paralleles. La datation d'un ancetre commun en 1979, date de debut de la construction de l'hopital, indiquerait une contamination precoce du reseau d'eau de l'hopital. Cette hypothese est soutenue par la presence d'un ilot genomique specifique de ST395 portant les genes codant 6 transporteurs du cuivre et associee a une resistance phenotypique a ce metal constituant les tuyaux du reseaux de distribution d'eau potable. Les isolats tardifs presentaient des signatures genomiques d'adaptation a l’infection chronique (alteration du lipopolysaccharide et de la porine OprD – objectivees phenotypiquement, et extinction de la surproduction de la pompe d’efflux MexAB-OprM – controlee par RT-qPCR) suite a des mutations independantes. Certaines de ces mutations ont ete associees a une perte de fitness bacterien. Nous emettons l’hypothese que l’emergence independante d’isolats adaptes a l’infection chronique, et ainsi l’accumulation de culs-de-sac epidemiologiques, a participe a l’epuisement de l’epidemie hospitaliere de P. aeruginosa ST395.
Simulating Solar Coronal Mass Ejections Constrained by Observations of Their Speed and Poloidal Flux

We demonstrate how the parameters of a Gibson-Low flux-rope-based coronal mass ejection (CME) can be constrained using remote observations. Our Multi-Scale Fluid-Kinetic Simulation Suite has been used to simulate the propagation of a CME in a data-driven solar corona background computed using the photospheric magnetogram data. We constrain the CME model parameters using the observations of such key CME properties as its speed, orientation, and poloidal flux. The speed and orientation are estimated using multi-viewpoint white-light coronagraph images. The reconnected magnetic flux in the area covered by the post-eruption arcade is used to estimate the poloidal flux in the CME flux rope. We simulate the partial halo CME on 2011 March 7 to demonstrate the efficiency of our approach. This CME erupted with the speed of 812 km s−1 and its poloidal flux, as estimated from source active region data, was 4.9 × 1021 Mx. Using our approach, we were able to simulate this CME with the speed 840 km s−1 and the poloidal flux of 5.1 × 1021 Mx, in remarkable agreement with the observations.
Perceive Where to Focus: Learning Visibility-Aware Part-Level Features for Partial Person Re-Identification

This paper considers a realistic problem in person re-identification (re-ID) task, i.e., partial re-ID. Under partial re-ID scenario, the images may contain a partial observation of a pedestrian. If we directly compare a partial pedestrian image with a holistic one, the extreme spatial misalignment significantly compromises the discriminative ability of the learned representation. We propose a Visibility-aware Part Model (VPM) for partial re-ID, which learns to perceive the visibility of regions through self-supervision. The visibility awareness allows VPM to extract region-level features and compare two images with focus on their shared regions (which are visible on both images). VPM gains two-fold benefit toward higher accuracy for partial re-ID. On the one hand, compared with learning a global feature, VPM learns region-level features and thus benefits from fine-grained information. On the other hand, with visibility awareness, VPM is capable to estimate the shared regions between two images and thus suppresses the spatial misalignment. Experimental results confirm that our method significantly improves the learned feature representation and the achieved accuracy is on par with the state of the art.