Miracle-dz/UniFAR-FTUs huggingface dataset:
Mesures et modélisation du travail de sortie de nanoparticules d'or fonctionnalisées et supportées

Le travail de sortie d’un metal est une propriete fondamentale en physico-chimie des materiaux. C’est l’energie necessaire pour extraire un electron depuis le niveau de Fermi vers le niveau du vide. Il est connu que cette grandeur depend de la nature du metal, mais aussi que d’autres parametres ont une influence notable. Ainsi ce travail de these montre comment le travail de sortie peut etre module par une couche de molecules auto assemblees sur la surface metallique, et comment il evolue quand le materiau est sous forme de nanoparticules. La presente etude se concentre sur des nanoparticules d’or (AuNPs) de diametres compris entre 10 et 60 nm, et etudie les effets de fonctionnalisation par quatre molecules : l’hexanedithiol (HDT), l’aminooctanethiol (AOT), l’acide mercaptohexadecanoique (MDHA) et le dodecanethiol (DDT). Apres une etude detaillee des morphologies des surfaces planes d’or fonctionnalisees par microscopie a force atomique (AFM), des mesures de travail de sortie sur ces surfaces sont effectuees par microscopie a sonde de Kelvin (KPFM). En comparant ces resultats a des mesures de photoemission (UPS), l’effet de chaque fonctionnalisation est mis en evidence. Par exemple, le travail de sortie d’une surface fonctionnalisee par MHDA diminue de -0.30 eV par rapport a une surface d’or non fonctionnalisee. Ces resultats montrent aussi l’effet sur le travail de sortie du temps de contact avec l’atmosphere ambiante. Ensuite, nous abordons le cas des AuNPs, synthetisees par voie colloidale, puis post-fonctionnalisees par AOT ou par MDHA. La fonctionnalisation des AuNPs est suivie par des mesures optiques basees sur la mesure du pic d’absorption (plasmon) des AuNPs dans le visible. Apres fonctionnalisation, leur travail de sortie est mesure par KPFM. Ces mesures mettent en evidence deux phenomenes : la modification du travail de sortie par la fonctionnalisation, ainsi qu’une variation en fonction de la taille de l’AuNP. Dans le but de comprendre precisement cet effet de taille, nos systemes ont ete modelises par une approche DFT (density functional theory), et les calculs de travaux de sortie ont ete confrontes aux mesures experimentales. Ces calculs sont en tres bon accord avec les resultats experimentaux, notamment sur l’evolution du travail de sortie en fonction de la taille des particules, d’environ 1 meV.nm 1.
Errata to “Evaluation of a Heterogeneous Multicore Architecture by Design and Test of an OFDM Receiver”

This paper presents an evaluation of a Heterogeneous Multicore Architecture (HMA) by implementing Orthogonal Frequency-Division Multiplexing (OFDM) receiver blocks as designs for the test of functionality. OFDM receiver consists of computationally intensive and general-purpose processing tasks that can provide maximum coverage to test and evaluate a massively-parallel as well as a general-purpose platform like the HMA. The blocks of the receiver are primarily designed by crafting template-based Coarse-Grained Reconfigurable Array (CGRA) devices and then arranging them in a sequence over a Network-on-Chip (NoC) structure along with a few RISC cores for complete OFDM processing. The OFDM blocks such as Fast Fourier Transform (FFT) and Time Synchronization are computationally intensive and require parallel processing. The OFDM receiver also contains tasks such as frequency offset estimation which require the processing of Taylor series and CORDIC algorithms that are serial in nature. Such a combination of serial and parallel algorithms can perform a thorough exploration and evaluation of almost all the design features of an HMA. The OFDM implementation has led to scale CGRAs to different dimensions, instantiate Processing Elements (PEs) as multiple arithmetic resources and to establish almost all possible ways of PE interconnections. It further explores time-multiplexed patterns for data placement in the CGRA memories. Nevertheless, the data can also be exchanged among different nodes over NoC structure simultaneously and independently by using direct memory access devices. In this experimental work, the performance of each CGRA, the collective performance of the whole platform and the NoC traffic are recorded in terms of the number of clock cycles and several high-level performance metrics. Today's HMAs are generally over or under resourced for the applications that they are designed for and thus not an optimal choice for the end user. Apart from the interesting comparisons to the other state-of-the-art, our experimental setup has provided important insight and guidelines that the designers can use to implement near-optimal solutions for their target applications.
Protein prenylation inhibitors reveal a novel role for RhoA and RhoC in trafficking of G protein-coupled receptors through recycling endosomes

Per the request of the author and advisor, and with the approval of the Graduate Education office, the following changes were made to this thesis: Replaced original page 1 with Errata Page 2. Replaced original pages 3-28 with Errata Pages 3 – 16. Replaced original pages 69-71 with Errata pages 17 – 19.
Biochemical and cell biological analysis of the mechanism of RNA interference in human cells

RNA interference (RNAi) in human cells is efficiently triggered by short interfering RNA (siRNA) duplexes of 19-24 base-pairs (bp), which mimic the double-stranded processing intermediates of the endogenous small RNA species, microRNAs (miRNAs). Single-stranded siRNAs and miRNAs are incorporated into Argonaute protein-based RNA silencing complexes, to mediate inactivation of complementary mRNAs by cleavage or translational repression. There are eight Argonaute proteins expressed in humans, four Ago and four Piwi subfamily members, however only one of the Ago proteins is capable of the small RNA-guided cleavage of target mRNA. While all Agos can repress mRNA translation, the precise mechanism of this regulation is unknown. The role of mammalian Piwi proteins in RNA silencing processes has not been addressed. MiRNAs are predicted to regulate expression of one-third of the human genes. In light of the growing biological significance of RNA silencing processes, the current study addressed the mechanism of RNAi in human, focusing on two key components of RNA silencing complexes, small RNAs and the Argonaute proteins.To examine the fate of small RNAs in human cell lysate recapitulating target RNA cleavage activity, stability and processing of the radioactively labeled single- and double-stranded small RNAs was monitored in time-course experiments. The RNA duplexes were stable in the extract and their termini were converted to 5' phosphate and 3' hydroxyl groups, similar to the endogenous small RNA intermediates. Single-stranded siRNAs were rapidly degraded. The efficacy of 5'-phosphorylated single- and double-stranded siRNAs was tested in the cell culture. The single-stranded siRNAs were sufficient to trigger RNAi in the cultured cells. This suggests, that although siRNA duplexes are the preferred triggers of RNAi, single-stranded siRNAs can bypass the regular assembly pathway of the RNA silencing complex, especially while being 5'-phosphorylated.To examine the expression pattern of Argonautes in human cell lines, levels of the individual transcripts were quantified by qRT-PCR. Agos were found expressed in multiple human cell lines, while Piwis were detected only in the control samples from testis and ovary tissue. To understand the functional differences between the four Ago proteins, the association of Agos with the endogenous miRNAs was examined. The results suggest, that miRNAs are incorporated indiscriminately of their sequence into the different Ago-containing silencing complexes. The restricted expression of Piwis is in agreement with the reports on their germline expression in mouse, and implicates involvement of the RNA silencing in germline-specific processes in human. To check if the Piwis are capable of siRNA-guided target cleavage, the tagged Piwi proteins were ectopically expressed and purified. None of the Piwis was catalytically active in the tested conditions. To allow investigation of the role of Piwi proteins in the testis tissue, individual Piwi-specific antibodies were raised and/or characterized.
A Conceptual Framework of Salafi Radicalization: An Underlying Theme and its Enablers

The religion-invoking violent extremism called “radical Islam” has become a global threat. In particular, a form of Sunni Muslim radicalism called Salafi radicalism—embraced by jihadist groups such as al Qaeda, the Taliban, and the Islamic State—has gained prominence. What role religious leaders play in causing this phenomenon is not well understood. To address this issue, I outline a novel theoretical framework for conceptualizing Salafi radicalism in terms of an underlying theme and its enablers. This proposal further divides radicalization processes into primary and secondary ones; the former are identified with the onset of radicalization in a community, and the latter develop in communities with longstanding exposure to the phenomenon. A new analysis of a 2013 Pew Research Center report suggests that sharia’s popularity in a community can make religious leaders and their radical ideas highly influential, while in communities where sharia has little influence, religious leaders and their radical ideas likewise lack influence. This article suggests the following primary explanation of the phenomenon: backed by the prestige and resources of Saudi Arabia, religious leaders have popularized the appealing theme of sharia as all-encompassing “divine law” to advance radical Islamist agendas. By identifying sharia as the theme and religious leaders as its enablers, such an explanation facilitates our understanding of the causes and backers of this religious radicalism.
Begging, Charity and Religion in Pre-Famine Ireland

Beggars and begging were ubiquitous features of pre-Famine Irish society, yet have gone largely unexamined by historians. Begging, Charity and Religion in Pre-Famine Ireland explores at length for the first time the complex cultures of mendicancy, as well as how wider societal perceptions of and responses to begging were framed by social class, gender and religion. The study breaks new ground in exploring the challenges inherent in defining and measuring begging and alms-giving in pre-Famine Ireland, as well as the disparate ways in which mendicants were perceived by contemporaries. A discussion of the evolving role of parish vestries in the life of pre-Famine communities facilitates an examination of corporate responses to beggary, while a comprehensive analysis of the mendicity society movement, which flourished throughout Ireland in the three decades following 1815, highlights the significance of charitable societies and associational culture in responding to the perceived threat of mendicancy. The instance of the mendicity societies illustrates the extent to which Irish commentators and social reformers were influenced by prevailing theories and practices in the transatlantic world regarding the management of the poor and deviant. Drawing on a wide range of sources previously unused for the study of poverty and welfare, this book makes an important contribution to modern Irish social and ecclesiastical history.
Susceptibilité génétique des variants EP300 et PCAF au carcinome hépatocellulaire et rôle de septine 9, PIAS1 et SUMO1 dans la réplication du virus de l'hépatite C

Le carcinome hepatocellulaire (CHC) est la tumeur maligne primitive du foie la plus frequente (90 % des cas). Le CHC est le cinquieme cancer par ordre de frequence a l'echelon mondial, la troisieme cause de deces par cancer dans le monde entier et son incidence est actuellement croissante. Parmi Les principaux facteurs predictifs de survenue de CHC ; les alterations genetiques, l'alcool et les infections par les virus des hepatites B (VHB) et C (VHC). Les travaux de these en cotutelle menes entre l’Universites Paris Sud 11-France et l’Universite Mohammed V- Rabat –MAROC ont porte essentiellement sur l’etude de deux facteurs de risque impliques dans le developpement du carcinome hepatocellulaire ; le polymorphisme genetique et l’infection par le virus de l’hepatite C. Dans un premier temps, ce travail de recherche s’est focalisee sur l’eventuelle relation pouvant liee les polymorphismes genetiques des genes PCAF, P300 au carcinome hepatocellulaire. Sur le plan genetique nous avons constate que les genotypes Val/Val de EP300 et Ser/Ser de PCAF apparaissent comme les plus associes a l’hepatocarcinome. Par ailleurs, ces derniers se trouvent associes d’une maniere significative au carcinome hepatocellulaire. Par la suite, notre travail a consiste a mieux caracteriser la variabilite genetique du HCV et l’epidemiologie des souches virales chez la population marocaine pour lesquelles peu de donnees etaient disponibles. Les analyses phylogenetiques des regions NS5B et E2 et les donnees epidemiologiques recueillies ont permis de repondre a ces questions. Enfin, La derniere partie des travaux de cette these vise a identifier des facteurs cellulaires essentiels a la replication du VHC, dans l’objectif de definir de nouvelles cibles therapeutiques pour le traitement des hepatites virales C. Nous avons pu identifier la septine 9 comme facteur cellulaire implique dans le cycle de vie virale du HCV, ainsi que les proteines PIAS1 et SUMO1 comme proteines regulatrices de la septine 9. De plus nous avons pu etablir la relation entre ces proteines cellulaires dont la presence est necessaire a la fois a la production des proteines virales ( CORE et E2) et a la replication du virus dans la cellule hote.
Ribosomal Resistance to Streptomycin in Strains Regenerated from Protoplasts of a Streptomycin-Susceptible Mutant Derived from a Streptomycin Producer

When protoplasts of streptomycin-sensitive Streptomyces griseus KSN were regenerated to the mycelial form, streptomycin-resistant cultures appeared at a high frequency (approximately 1%). The resistance mechanism of the seregenerated cultures was different from that of ancestral streptomycin-producing Streptomyces griseus HUT 6037, from which the parent S. griseus KSN was derived. While the resistance to streptomycin of S. griseus HUT 6037 was due mainly to streptomycin-phosphorylating activity of streptomycin 6-kinase produced in the cells, the streptomycin-resistant cultures regenerated from protoplasts produced no streptomycin 6-kinase but the ribosomes changed and became resistant to streptomycin. In highly streptomycin-resistant cultures regenerated, one of the 30S ribosomal proteins was altered in electrophoretic mobility as compared to the corresponding protein of S. griseus KSN
The role of the construction sector in influencing natural resource use, structural change, and industrial development in Zambia

The construction sector plays a critical role in delivering quality infrastructure, which in turn influences the use of natural resource revenues towards achieving structural change and industrial development. We use industrial organization and political economy lenses to describe and understand the organization of and changes in the construction industry in Zambia, focusing on demand-side factors; supply-side issues; market interactions through pricing and costs; and public institutions, regulations, policies, and structures. We establish the main firm-level, industry-wide, and macroeconomic bottlenecks affecting Zambia's construction sector and offer options for dealing with the key bottlenecks. In particular, we suggest: institutional reforms and legal and regulatory changes governing procurement and contracting rules and systems; training and other capacity-building programmes; greater access for local contractors to existing financing sources, including the Skill Development Levy; a review and update of the local content and subcontracting strategy and policy; and state-supported and -financed/-resourced research and development programmes.
Aplicación del modelo logístico para describir la curva de crecimiento en perros de diferentes razas

Objective. To model the growth in dogs of different size and breeds that during their development showed a relative body weight according to the standards of their racial group. Materials and methods. The data used were obtained from the Canine Research Center (CIC), property of Empresa Solla S.A. , located in the municipality of Rionegro (Antioquia, Colombia). The parameters of the growth curve were defined based on the logistic model using the procedure PROC NLIN of the SAS. Results. The adult weight (a) ranged from 2.12 Kg (York Shire Terrier) to 32.88 Kg (Weimaraner). For small, medium and large breeds, growth rates (1/b) during the exponential phase ranged between 9.9118. 91%, 9.12-13.83% and, 8.17-14.38%, respectively, and the average age at which 50% of the adult weight was reached (x 0 ) was 3.49±0.03, 4.21±0.42 y 5.27±0.86 months, correspondingly. Large dog breeds reached maturity (T 99 ) later than smaller breeds, 14.37±1.79 vs. 9.46±1.63 mo. Conclusions. The logistic model was able to describe the growth in dogs of different size, however, a larger sample size will improve its predictive ability, given the individual variability that characterizes growth.
The expression of embryo maturation genes in wheat and the role of abscisic acid

approved: Redacted for Privacy I A set of genes which show developmental and tissue specificity are expressed late in embryo maturation during grain formation in wheat (Triticum aestivum). Two members of this maturation gene set (MGS) are Em and triticin, a 7S globulin. Results presented here show that during embryogenesis, the expression of Em mRNA and polypeptide is temporally associated with increasing levels of the plant growth regulator abscisic acid (ABA). In the absence of elevated ABA levels, neither the mRNA nor the polypeptide for Em or triticin are detected at other developmental stages or in non-embryonic tissues. In situ hybridization shows that Em mRNA is localized in the embryo axis of the developing grain with high amounts concentrated in the shoot and root apices. Absence of Em mRNA in the scutellum and endosperm, the embryo storage organs, suggests that the function of Em in not one of a storage protein. However, mRNA levels of Em and triticin increase in response to higher levels of ABA at other stages of vegetative development. When ABA is supplied to germinating seedlings, mRNA for both Em and triticin accumulate. Some seed globulin proteins also accumulate in germinating seedlings after exposure to ABA. Em mRNA accumulation coincides with the pattern of increasing endogenous ABA concentrations in dehydrating seedling shoots. However, neither Em nor seed globulin polypeptides are detected in dehydrating tissue. These results suggest that ABA promotes MGS transcription or mRNA stability, in tissues other than embryos, but other factors control tissue specific expression at the polypeptide level. Desiccation of the embryo during normal grain development does not appear to be a trigger to prevent expression of MGS mRNA in response to ABA in non-embryonic tissue. However, desiccation may serve to alter the metabolic environment, preventing MGS polypeptides from accumulating. The implications of these findings on the proposed function of the MGS gene products and their regulation during development are discussed. THE EXPRESSION OF EMBRYO MATURATION GENES IN WHEAT AND THE ROLE OF ABSCISIC ACID
Zipporah: a Fast and Scalable Data Cleaning System for Noisy Web-Crawled Parallel Corpora

We introduce Zipporah, a fast and scalable data cleaning system. We propose a novel type of bag-of-words translation feature, and train logistic regression models to classify good data and synthetic noisy data in the proposed feature space. The trained model is used to score parallel sentences in the data pool for selection. As shown in experiments, Zipporah selects a high-quality parallel corpus from a large, mixed quality data pool. In particular, for one noisy dataset, Zipporah achieves a 2.1 BLEU score improvement with using 1/5 of the data over using the entire corpus.
Abstract 1893: A computational method for somatic versus germline variant status determination from targeted next-generation sequencing of clinical cancer specimens without a matched normal control

Background: A key constraint in genomic testing in oncology is that matched normal specimens are not commonly obtained in clinical practice. Thus, while most clinically relevant genomic alterations have been previously characterized and do not require normal tissue for interpretation, interpretation of novel variants whose somatic status is unknown is limited. We describe our approach to predicting somatic status of genomic alterations from tumor tissue alone in a CLIA-certified, NGS-based test that interrogates 236 cancer-related genes. Methods: For each sample, we obtain a genome-wide “CGH” profile based on coverage and allele frequencies (AF) at >3,500 SNPs, which is segmented and modeled to estimate the tumor purity (p), copy number (C), and minor allele count (M) at each segment. A variant9s measured AF is compared to expectation: AFgermline = (pM+1-p)/(pC+2(1-p)) versus AFsomatic = pM/(pC+2(1-p)) and prediction is made with statistical confidence based on read depth and local variability of SNP AF. Results: For validation, we examined samples from 30 lung & colon cancer patients, where we sequenced tumors and matched-normal tissue. More broadly, we examined predictions for 17 somatic hotspot mutations and 20 common germline SNPs in 2,578 clinical cancer specimens. Finally, to assess the impact of stromal admixture, we examined 3 cell lines, which were titrated with their matched normal to 6 levels (10% to 75%). Overall, predictions were made in up to 85% of cases, with 95%-99% of variants predicted correctly: Conclusions: This method leverages deep NGS to predict variant somatic status without a matched-normal control. It supports functional prioritization and interpretation of alterations discovered on routine testing and can indicate additional work-up if germline risk variants are found. When optimized and fully validated, it may inform clinical decision making and expand treatment choices for cancer patients. Citation Format: James X. Sun, Garrett Frampton, Kai Wang, Jeffrey S. Ross, Vincent A. Miller, Philip J. Stephens, Doron Lipson, Roman Yelensky. A computational method for somatic versus germline variant status determination from targeted next-generation sequencing of clinical cancer specimens without a matched normal control. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 1893. doi:10.1158/1538-7445.AM2014-1893