Miracle-dz/UniFAR-FTUs huggingface dataset:
Untersuchungen zur Struktur und Spezifität der Phycobiliproteinlyase CPES aus Guillardia theta

Cryptophyten verwenden neben Chlorophyll zusatzliche Lichtsammelproteine fur die Photo-synthese – die Phycobiliproteine (PBP). In Cyanobakterien, Rotalgen und Glaukophyten sind PBP ebenfalls ubiquitar verbreitet. Fur den Zweck der Lichtsammlung tragen die PBP- Untereinheiten kovalent gebundene offenkettige Tetrapyrrol-Chromophore an konservierten Cysteinresten. Diese Phycobiline sind in der Lage, grunes Licht zu absorbieren und es fur die Photosynthese zur Verfugung zu stellen. Die Fahigkeit zur Photosynthese erlangten Crypto-phyten bei der sekundaren Endosymbiose durch Aufnahme einer fruheren Rotalge. Die evolutionare Entwicklung brachte schlieslich modifizierte PBP hervor. In Gegensatz zu ande-ren Organismen liegen die PBP in Cryptophyten in loslicher Form im Thylakoidlumen des Plastiden vor. Cryptophyten besitzen lediglich einen Typ an PBP, Guillardia theta verwendet Phycoerythrin PE545. Die α-Untereinheiten sind jeweils mit einem Molekul 15,16-Dihydrobi-liverdin (DHBV) und die β-Untereinheiten mit drei Molekulen Phycoerythrobilin (PEB) chromophoryliert. Die Chromophorylierung cryptophytischer Apo-PBP ist bisher wenig un-tersucht und verstanden. Aus Cyanobakterien ist jedoch bekannt, dass die Chromophorylie-rung haufig mit Hilfe von Phycobiliproteinlyasen (PBP Lyasen) stattfindet, welche die Phyco-bilinubertragung unterstutzen. In der vorliegenden Arbeit erfolgte die funktionelle Charakterisierung der eukaryotischen S-Typ-PBP Lyase GtCPES aus G. theta. Mittels Fluoreszenzspektroskopie und Zink-induzierter Fluoreszenz konnte gezeigt werden, dass GtCPES den Transfer von 3(Z)-PEB auf Cys82 der PBP-β-Untereinheit aus Prochlorococcus marinus MED4 (PmCpeB) vermittelt. An der PEB-Bindung sowie am -Transfer beteiligte Aminosauren wurden mit Hilfe Zielgerichteter Muta-genese identifiziert. Anhand spektroskopischer Binde- und Transferstudien mit den Protein-varianten wurden drei Aminosauren in der Ligandenbindetasche ermittelt, die relevant fur die Bindung sind (Trp69, Glu136, Glu168). Diese koordinieren vermutlich PEB in der Bindetasche und stabilisieren somit die Konformation. Zusatzlich konnten zwei im PEB-Transfer involvierte Aminosauren eindeutig identifiziert werden (Trp75, Ser150). Trp75 kommt dabei eine essenzielle Bedeutung fur den Transfer zu. Des Weiteren konnte gezeigt werden, dass Met67 fur die auf PEB und DHBV beschrankte Substratspezifitat von GtCPES verantwortlich ist. Die Variante GtCPES_M67A bindet sowohl PEB als auch das rigide Phycocyanobilin (PCB) stabil unter Bildung eines farbigen Komplexes in vitro und in vivo in Escherichia coli. GtCPES_M67A scheint zudem in der Lage zu sein, PCB auf geeignete Apo-Proteine zu transfe-rieren. Neben der sterischen und elektrostatischen Umgebung entscheidet damit zusatzlich die Substratspezifitat der PBP Lyase uber die gebundenen Chromophore am PBP.
Improving performance and transferability of small mammal species distribution models

ABSTRACT In theory, interpretation and transferability of species distribution models (SDMs) should be improved by including abiotic and biotic factors that directly influence a species’ fundamental niche. We investigated whether adding topographic, soil and vegetation variables to a climate-only model improved model performance and predictive capacity for four coastal small mammal species. Adding landscape variables improved the structural goodness of fit for all four species (e.g. 2.6–47.6% increase in deviance explained), and the information-theoretic rankings (based on AICc, BIC and DIC) for the wet-heath specialist (Muridae, Rattus lutreolus lutreolus) and peramelid (Peramelidae, Isoodon obesulus obesulus). For the latter species, improved model performance successfully coincided with improved predictive capacity in the out-of-region validation (increase in the area under the curve, AUC). However, this result was poorly supported by trends in the successful classification of absences (specificity) indicating a modelling bias caused by low prevalence of species occurrence. Across all SDMs, additional abiotic and biotic landscape variables contributed between 3.7 and 14.9% of accumulative deviance explained. Our results illustrate increased model fit and transferability for select species, highlighting the potential for landscape variables that represent resources to better represent the fundamental niche in SDMs.
Socio-technical system analysis of indigenous crop production practices for banana (Musa spp.)

ABSTRACT The present study, undertaken in the state of Kerala, India, documented 111 Indigenous Crop Production Practices (ICPPs; traditional practices) for banana and most of the practices were registered in the technology dimensions of seeds and seedlings (19%), manuring (19%), and planting in main field (15%). Of the 111 practices, 35 were selected for analysis of rationality, and for knowledge and adoption among farmers. Of the 35 practices, 27 (77%) were rated as rational and the scientific rationale/operational principles were elucidated in the study, revealing a strong scientific base for these practices. The knowledge of and the adoption of these traditional practices by farmers was found to be good. The effectiveness of the practices, as perceived by the farmers who had adopted them, were analysed for 21 practices, and it was found that majority (86%) of the traditional practices for banana production were effective. The study revealed that many indigenous practices for banana were both rational and effective. These practices require urgent attention in order to integrate them with modern technologies, which in turn would promote sustainable crop production and maintenance of ecosystem integrity. Abbreviation: ITK: indigenous technical knowledge
Section A. Physiology. Ruminant metabolism in relation to the synthesis and secretion of milk fat

Introduction 139 Structure and composition of milk fat 139 Milk fat globule 139 Phospholipids 141 Triglycerides 142 Synthesis and secretion of milk fat 144 Intramammary synthesis of fatty acids 144 Malonyl pathway 145 Non-malonyl pathways 147 Contribution of plasma lipids to milk fat 148 Synthesis of milk triglycerides, phospholipids and cholesterol esters 149 Formation and secretion of milk fat globules 150
ANALISIS SKALA KEMAMPUAN MAHASISWA KIMIA MELALUI TES ENTRY BEHAVIOUR METODE COMPUTERIZE ASSISTED TEST (CAT) MENGGUNAKAN ITEM RESPONS THEORY (IRT)

Penelitian ini bertujuan untuk menganalisis Skala Kemampuan Mahasiswa Kimia Melalui Tes Entry Behaviour Metode Computerize Assisted Test (CAT) Menggunakan Item Respons Theory (IRT) Model Logistik 1-Parameter. Subjek penelitian adalah seluruh lembar jawaban peserta Tes Entry Behaviour Mahasiswa Program Studi Pendidikan Kimia Tahun 2019. Penelitian ini merupakan penelitian kuantitatif menggunakan pendekatan ex-post facto. Hasil analisis dengan pendekatan teori tes klasik menunjukkan 79,5% butir memiliki tingkat kesulitan butir berfungsi baik, 57% butir daya bedanya belum memenuhi syarat, dan 72% butir memiliki pengecoh berfungsi baik dengan indeks reliabilitas tes 0,832. Analisis dengan pendekatan teori respons butir menunjukkan terdapat 11 (27,5%) butir soal cocok (fit) dengan model, fungsi informasi maksimum 5,48 pada θ = -0,21, dan besarnya kesalahan pengukuran (SEM) 0,21.
Learning Multimodal Digital Models of Disease Progression from Longitudinal Data : Methods & Algorithms for the Description, Prediction and Simulation of Alzheimer’s Disease Progression

La these s'interesse a l'apprentissage statistique de modeles digitaux de progression des maladies neurodegeneratives, en particulier la maladie d'Alzheimer. Ces modeles ont pour but de reconstruire la dynamique complexe et heterogene de l'evolution de la structure, des fonctions et des facultes cognitives du cerveau, a un niveau moyenne mais egalement a l'echelle individuelle. Pour repondre a cet objectif, la these considere un modele generatif a effets mixtes qui, a partir de donnees longitudinales, c'est a dire des observations repetees pour chaque patient, et eventuellement multimodales, recombine les trajectoires spatiotemporelles individuelles en un scenario moyen de progression de la maladie, estimant conjointement la variabilite de cette progression caracteristique. Cette variabilite est le resultat du non alignement temporel (en terme de vitesse de progression et âge de debut de la maladie) et d'une variabilite spatiale qui prend la forme d'une modification de la sequence d'evenements qui interviennent durant l'apparition et la progression de la maladie. Les differentes parties de la these forment une suite logique, depuis la problematique medicale, en passant par la description du modele statistique associee, l'application de celui-ci pour la description de l'evolution de la maladie d'Alzheimer, et, enfin, le developpement d'outils numeriques a destination du corps medical pour tirer pleinement parti des methodes presentees.
IN VITRO ANTIBACTERIAL, ANTIOXIDANT, CYTOGENOTOXIC AND NUTRITIONAL VALUE OF ALOE BARBADENSIS MILL. (ASPHODELACEAE)

the in vitro antibacterial, antioxidant, nutritional and cytogenotoxic potentials of Aloe barbadensis (AB) root extract. The antimicrobial activity of AB was determined using agar well diffusion and microdilution techniques while the nutritional analyses were done using standard procedures. The antioxidant activities were evaluated via the lipid peroxidation, 1, 1, diphenyl-2-picrlhydrazyl (DPPH) and ferric reducing power (FRAP) assays. The cytogenotoxic effects were assessed using the Allium cepa and Sorghum assays. Five test bacterial isolates: Escherichia coli, Klebsiella pneumoniae, Proteus mirabilis, Pseudomonas aeruginosa and Staphylococcus saprophyticus) were found susceptible to the ethanolic extract of AB root. The extract at 50 mg/ml recorded the highest zone of inhibition (25.00±1.73 mm) against S. saprophyticus . The nutritional analysis gave a nitrogen free extract value of 24.66%, 30.05% crude fibre, 15.14 mg/kg of Na, 2.01 mg/kg of Mg, 37.42 mg/kg of Fe and 0.02 mg.kg of Zn. The fractions had antiradical activity in the lipid peroxidation, DPPH and FRAP assays. The ethanolic extract induced some chromosomal aberrations in the root tip cells of Allium cepa . The ethanolic extract had the highest (0.13±0.09 mm) antiproliferative activity at 20 mg/kg in the Sorghum bicolor assay. The relatively high nutrient content may be a possible mechanism for the aphrodisiac property of the plant. The results of the biological activities of AB root is an indication of its potential use in drug development for the management of infectious diseases and other related ailments.
3D convolutional neural networks for Alzheimer’s disease classification

Dementia of the Alzheimer’s type (DAT) is a neurodegenerative disease characterized by abnormal brain metabolism and structural brain atrophy. These functional and structural changes can be observed in images acquired using 18F-fluorodeoxyglucose positron emission tomography (FDG-PET) and structural magnetic resonance imaging (MRI). Traditional machine learning framework for DAT classification often involves time-consuming segmentation of brain images as part of the feature extraction process, while deep neural networks can learn DAT-related patterns directly from brain images to generate DAT probability scores. In this thesis, we design 3D convolutional neural networks (CNN) for two applications: classification and segmentation. We design classification networks for single modality use and perform comprehensive evaluation by measuring the performance of our networks on images along the entire DAT spectrum. To support traditional DAT classification framework, we design a fast and accurate segmentation pipeline. We propose a hemisphere-based approach where we train networks to localize and segment hemispheres.
INCREASING STUDENT VOCABULARY BY USING CROSSWORD PUZZLE EIGHT GRADE STUDENTS OF SMP NEGERI 1 GALANG

The objective of the research is to prove whether the use of crossword puzzle is effective to increase students’ vocabulary. This pre-experimental study uses 23 students as a sample. They are grade VIII c of SMP Negeri 1 Galang. The procedure of this research consists of pretest, treatment, and posttest. The result of the analysis shows that crossword puzzle contributes greatly to increse the students’ vocabulary. It can be seen by the difference of the mean score between pre-test and post-test. The mean score of pre-test is 67.30 while in the post-test increase up to 90.87. The data of this research are analyzed by using SPSS Program version 16.0. Then the data of both tests are analyzed by using T-test, and the result shows that the T-test value 8.502 is high than T-table value 2.074. It can be inferred that crossword puzzle is very effective to increase students’ vocabulary. Keywords: Increasing, Crossword Puzzle, Vocabulary.
Formal modeling and analysis of resource usage and sharing in distributed software systems

AB: This thesis investigates problems of formal, mathematically based, representation and analysis of controlled usage and sharing of resources in distributed software systems. We present a model for confidential name passing, and a model for controlled resource usage. For the second model we also introduce a type system for performing a static verification that can ensure absence of unauthorized usages of resources in the system. Accepted by the Scientific Board on, ASB: September 05, 2019
Effects of Salinity and pH on the Infective Capacity of Romanomermis iyengari1 and Romanomermis culicivorax1 in Larvae of Culex quinquefasciatus2 Mosquito

Abstract. Effects of salinity and pH were assessed on the infective capacity of parasitic nematodes of mosquitoes Romanomermis culicivorax Ross & Smith and Romanomermis iyengari (Welch), on larvae of southern house mosquito, Culex quinquefasciatus Say. Thirteen pH levels (3.6, 3.8, 4.0, 4.5, 5.0, 5.5, 6.0, 6.5, 7.0, 7.5, 8.0, 8.2, and 8.4) were evaluated. Six salinity levels (NaCl concentrations) were evaluated, with values of 0.01 M (584 mg/L), 0.02 M (1,169 mg/L), 0.03 M (1,753) mg/L), 0.04 M (2,338 mg/L), 0.05 M (2,922 mg/L), and a 0.00 M check, with three replications. Percentage of infection (of parasitized larvae) and infestation intensity (average nematodes parasitizing a mosquito larva) were recorded for both factors. To determine effects of pH and salinity on percentage of infection and infestation intensity, a sample (n = 20, IV instar) of larvae surviving at high salinity levels was extracted 5 days after application. The greatest percentage of infection statistically significant in R. iyengari was 75 to 91.7 for pH 5.0 to 7.5, and 86.7 to 100 for R. culicivorax between pH 6.0 and 7.0. The greatest infestation intensity statistically significant in R. iyengari was 4.42 to 8.45 between pH 4.5 and 8.0. The greatest levels of infestation statistically significant in R. culicivorax were between pH 5.0 and 7.5 with 3.07 and 3.63 nematodes per mosquito larva.
Dihydrofolate Reductase Thermosensitive (ts-dfrA) Mutant Induces Dihydrofolate Overproduction by Lactobacillus plantarum

ABSTRACT Dihydrofolate (dihydrofolic acid, vitamin B9) is one of the principle reduced forms of folates, which is converted to tetrahydrofolate by dihydrofolate reductase (DHFR). The aim of the present study was to overproduce total folate by inducing accumulation of dihydrofolate (DHF) due to inhibition of DHFR in a thermosensitive mutant (TS) of Lactobacillus plantarum. This mutant (TS34) was obtained by UV-mutagenesis of L. plantarum wild-type parent strain (HMA07) isolated from fermented sausage. The mutant TS34 was characterized by its ability to grow at 30°C but not at 40°C. Strain HMA07 and its mutant TS34 were identified by determining partial sequence of 16S rRNA gene. A single C→T exchange in the dfrA (dihydrofolate reductase gene) at nucleotide 184 was detected. This exchange led to the conversion of leucine (L) to phenylalanine (F) at the position 62 in amino acid sequence (L62F transition). TS43 showed significant (p < 0.05) reduction in DHFR activity from 1.51 to 0.06 Unit/mg protein, resulting in increasing DHF amount at the expense of THF. Accordingly, total folate production by the mutant TS34 (in two-stage fermentation process with temperature shift-up from 30°C to 40°C) increased by three-fold compared with the parental strain HMA07. In conclusion, thermosensitive mutation in dfrA caused inhibition of DHFR and resulted in accumulation of DHF. The technique described here could be considered as novel strategy for overproduction of DHF in two-stage fermentation process.
Sound-Generating Mechanisms in Fishes: A Unique Diversity in Vertebrates

Fishes have evolved the largest diversity of sonic organs among vertebrates. The main group of sound producing mechanisms is based on the swimbladder. These can be vibrated by intrinsic drumming muscles located in the wall of the swimbladder (toadfishes, searobins), or by extrinsic drumming muscles, which originate on structures such as the skull, vertebral processes or body wall musculature. Extrinsic drumming muscles insert either directly on the swimbladder (e.g. pimelodid catfish, tiger perches) or vibrate the swimbladder indirectly either via broad tendons (piranhas, drums) or via bony plates (elastic springs in doradid, mochokids and ariid catfishes). Pectoral sound-producing mechanisms include vibration of the pectoral girdle (sculpins), rubbing of the enhanced pectoral spine in a groove of the shoulder girdle (catfishes), and plucking of enhanced fin tendons (croaking gouramis). In addition, sounds can be produced by other morphological structures such as dorsal fin spines, neck vertebrae and pharyngeal teeth grating. In a few taxa, such as catfishes, two different sound-producing mechanisms (swimbladder and pectoral) are present simultaneously. In several other well-known vocalizing taxa (damselfishes, gobies, loaches) the mechanisms remain unidentified. Sound-generating mechanisms may be similarly developed in males and females (croaking gourami) or sexually dimorphic, in which case they are always better developed in males. In toadfishes males possess a relatively higher sonic muscle mass than females, whereas in some drum species muscles are totally absent in females. In the midshipman Porichthys *Corresponding Author 4 Communication in Fishes notatus, territorial males possess larger sonic muscles than parasitic sneaker males, which steal fertilizations. In drums sonic musculature hypertrophies seasonally, a process apparently controlled by the hormone testosterone. Drumming muscles vibrate the swimbladder at high rates (50–250 Hz), which results in emission of low-frequency harmonic sounds in which the contraction rates constitutes the fundamental frequency. In contrast, rubbing of bony structures against each other (stridulation) or tendon plucking results in production of broad-band pulsatile sounds with dominant frequencies at or above 1 kHz. The inability of fishes to vary their sound emissions by air flow modulations, as do birds and mammals, reduces the variation of sounds to differences in intensity, rate, and number and duration of pulses. Nevertheless, some species can emit up to five different sound types in different behavioral contexts.
A Usability Inspection Approach to Assist in the Software Development Process

— Several approaches have been proposed to ensure the quality of interactive systems. However, interactive systems continue to reach users with malfunctions, such as usability, communicability and interaction errors. Researches show that the lack of usability knowledge in software development organizations is an obstacle for usability evaluation. Our research goal is to popularize usability inspections so that even novice inspectors are able to perform it. Aiming to provide an approach to be used during the development process of web application, we have proposed the WE-QT technique. We are using an experimental methodology to evolve our technique and transfer it from the academy to industry. This paper presents a new comparative study; the results show that WE-QT technique is more efficient than and as effective as the compared technique.
An SRC Working Paper

This paper seeks to identify and characterize research needs in the basic physical sciences that are required to sustain the exponential progress in nanoelectronics. We believe that increased work in the physical sciences is essential to achieve ultimate limits for current integrated circuit technologies. Moreover, we believe that basic research is required to realize the opportunities for the creation of and transition to new nanoelectronic technologies that could offer unparalleled advances in device density and performance. For the first time, the 1999 International Technology Roadmap for Semiconductors (ITRS) recognized technical barriers having no known solutions that are on the five-to-ten year implementation horizon. It is our thesis that if these barriers are to be bridged, the knowledge base in the physical sciences must be enhanced. Herein, we give examples of areas where additional research is needed to retain the current pace of progress of the semiconductor industry. We also argue that increased research in the physical sciences can provide the basis for a continuation of the unprecedented economic growth of the information technologies by enabling the creation of radical new devices, processes, and systems whose performance may ultimately be superior to that achievable through technology scaling.
Computational interaction techniques for 3D selection, manipulation and navigation in immersive VR

3D interaction provides a natural interplay for HCI. Many techniques involving diverse sets of hardware and software components have been proposed, which has generated an explosion of Interaction Techniques (ITes), Interactive Tasks (ITas) and input devices, increasing thus the heterogeneity of tools in 3D User Interfaces (3DUIs). Moreover, most of those techniques are based on general formulations that fail in fully exploiting human capabilities for interaction. This is because while 3D interaction enables naturalness, it also produces complexity and limitations when using 3DUIs. In this thesis, we aim to generate approaches that better exploit the high potential human capabilities for interaction by combining human factors, mathematical formalizations and computational methods. Our approach is focussed on the exploration of the close coupling between specific ITes and ITas while addressing common issues of 3D interactions. We specifically focused on the stages of interaction within Basic Interaction Tasks (BITas) i.e., data input, manipulation, navigation and selection. Common limitations of these tasks are: (1) the complexity of mapping generation for input devices, (2) fatigue in mid-air object manipulation, (3) space constraints in VR navigation; and (4) low accuracy in 3D mid-air selection. Along with two chapters of introduction and background, this thesis presents five main works. Chapter 3 focusses on the design of mid-air gesture mappings based on human tacit knowledge. Chapter 4 presents a solution to address user fatigue in mid-air object manipulation. Chapter 5 is focused on addressing space limitations in VR navigation. Chapter 6 describes an analysis and a correction method to address Drift effects involved in scale-adaptive VR navigation; and Chapter 7 presents a hybrid technique 3D/2D that allows for precise selection of virtual objects in highly dense environments (e.g., point clouds). Finally, we conclude discussing how the contributions obtained from this exploration, provide techniques and guidelines to design more natural 3DUIs.