Miracle-dz/UniFAR-FTUs huggingface dataset:
Indirect Allospecificity Rejection by Regulatory CD4 T Cells with Abrogation of Antibody-Mediated Allograft

Alloantibody is an important effector mechanism for allograft rejection. In this study, we tested the hypothesis that regulatory T cells with indirect allospeciﬁcity can prevent humoral rejection by using a rat transplant model in which acute rejection of MHC class I-disparate PVG.R8 heart grafts by PVG.RT1 u recipients is mediated by alloantibody and is dependent upon help from CD4 T cells that can recognize the disparate MHC alloantigen only via the indirect pathway. Pretransplant treatment of PVG.RT1 u recipients with anti-CD4 mAb plus donor-speciﬁc transfusion abrogated alloantibody production and prolonged PVG.R8 graft survival indeﬁnitely. Naive syngeneic splenocytes injected into tolerant animals did not effect heart graft rejection, suggesting the presence of regulatory mechanisms. Adoptive transfer experiments into CD4 T cell-reconstituted, congenitally athymic recipients conﬁrmed that regulation was mediated by CD4 T cells and was alloantigen-speciﬁc. CD4 T cell regulation could be broken in tolerant animals either by immunizing with an immunodominant linear allopeptide or by depleting tolerant CD4 T cells, but surprisingly this resulted in neither alloantibody generation nor graft rejection. These ﬁndings demonstrate that anti-CD4 plus donor-speciﬁc transfusion treatment results in the development of CD4 regulatory T cells that recognize alloantigens via the indirect pathway and act in an Ag-speciﬁc manner to prevent alloantibody-mediated rejection. Their development is associated with intrinsic tolerance within the alloantigen-speciﬁc B cell compartment that persists after T cell help is made available. The Journal of Immunology, 2007, 178: 2221–2228.
Expression of key synaptic proteins in Zebrafish (Danio Rerio) brain following caloric restriction and its mimetic and their relationship with gender

iii ÖZET. v ACKNOWLEDGEMENT . vii TABLE OF CONTENTS . ix LIST OF FIGURES . xiv LIST OF TABLES . xvi Abbreviations . xvii CHAPTER 1 . 1
Adaptive Potential of Fall Armyworm (Lepidoptera: Noctuidae) Limits Bt Trait Durability in Brazil

The fall armyworm, Spodoptera frugiperda (J. E. Smith 1797) (Lepidoptera: Noctuidae), is the most important corn pest in South America. Larvae feed mostly on leaves, but also ears when population densities are high. This pest has been historically controlled with insecticide applications, but many cases of resistance have limited their efficacy. Transgenic corn varieties expressing Bacillus thuringiensis proteins (Bt corn) have been a widely adopted alternative to insecticides and, in the past 8 yr, have been the primary technology for fall armyworm control in Brazil. Because transgenic varieties require 10–15 yr to be developed and fall armyworm has quickly evolved resistance to most commercially released Bt corn hybrids, strategies for Bt trait durability are paramount. Most of the Bt corn hybrids lost their ability to control fall armyworm in just 3 yr after their release in Brazil. Here we summarize what is known about Bt resistance in fall armyworm in Brazil, a phenomenon perhaps never seen before in any part of the world. Furthermore, we suggest that the interactions between management practices adopted (or not adopted, e.g., refuge compliance) to delay the evolution of resistance and the ecological and evolutionary characteristics of fall armyworm are driving the rapid evolution of resistance to Bt corn in Brazil. As newer products emerge in the market, careful consideration will be needed to maximize trait durability.
The effect of pre‐release captivity on the stress physiology of a reintroduced population of wild eastern bettongs

Stress is important in reintroduction biology because it can influence mortality, dispersal and recruitment and determine establishment success. As stress is unavoidable during reintroduction, it requires deliberate management. Release tactics (e.g. ‘delayed- and immediate-release’) are often selected specifically based on their presumed effect on physiological stress, yet, the actual physiological effects are seldom tested. Delayed-release involves pre-release confinement (in situ), or captivity (ex situ), which can improve post-release performance in some cases, or induce a detrimental effect in others, especially in wild animals. Quarantine is another common pre-release practice that requires captivity/confinement carrying similar post-release physiological implications. We use faecal glucocorticoid metabolite concentrations (FGM) to evaluate how a delayed-release involving 95–345 days in captivity influences the stress physiology of wild eastern bettongs (Bettongia gaimardi), compared to an immediate-release (within 24 h of capture), across the initial 18 months post-release. The results suggest that FGM concentrations were relatively higher in the delayed-release group at release, but significantly lower after ca. 2 months of release. We assessed seasonal fluctuations in FGM concentrations, the effect of release tactics on in-trap behaviour, and the relationship between those behaviours and FGM concentrations. We found that FGM concentrations fluctuated seasonally, but release tactics did not influence behaviour, and that behavioural variations had no relationship with FGM concentrations. Overall our results, coupled with previous research, suggest that an immediate-release is preferable when quarantine is not required.
Phosphorus use efficiency and critical P content of stevia grown in acid and non-calcareous soils of Bangladesh

Knowledge of phosphorus (P) uptake and its use efficiency by crop plants is essential for adequate management of the plant nutrients to sustain food production with a minimal environmental impact. To study the effects of P on the growth, leaf biomass production, P content and uptake and to estimate P use efficiency (PUE), minimum P requirement and critical leaf P content of stevia, a pot experiment was conducted in the net house of the Department of Agricultural Chemistry, Bangladesh Agricultural University following completely randomized design (CRD) with three replications in acid and non-calcareous soils of Bangladesh. The applied treatments was six viz. 0 (P 0 ), 25 (P 25 ), 50 (P 50 ), 75 (P 75 ), 100 (P 100 ) and 150 (P 150 ) kg P ha -1 . Plant samples were collected at 15 days interval to obtain different parameters. Collective results indicated that significantly highest values of different parameters were obtained with P @ 100 kg ha -1 and the lowest from P control. Phosphorus application increased leaf dry yield at harvest by 55 to 510% in acid soil and 70 to 488% in non-calcareous soil over control. The rapid growth of the plant was recorded at the later stages (30 to 60 days after planting). Phosphorus content and uptake was directly proportional with the increased levels of P except the treatment P 150 in both soils. Maximum PUE and fertilizer P use efficiency (FPUE) was observed at P 100 treatment. Critical P content was estimated to be ca 0.19 and 0.30% in the leaves of stevia plants grown in acid and non-calcareous soils, respectively. For maximum leaf biomass production of stevia grown in acid and non-calcareous soils, the minimum requirement of P was also estimated to be ca 109 and 104 kg ha -1 , respectively. The information of this finding would contribute to optimize the soil P use and improve fertilizer management for stevia cultivation. Res. Agric. , Livest. Fish.4(2): 55-68, August 2017
Behavioral and Electrophysiological Activity of the Racemate and Enantiomers of a Monofluorinated Analog of European Corn Borer (Lepidoptera: Pyralidae) Sex Pheromone

The racemate and individual enantiomers of 2-fluoro-Z-11-tetradecenyl acetate (2F-Z-11), analogs of a European corn borer moth, Ostrinia nubilalis (Hubner), female sex pheromone were compared with .
The Recognition and Mobility of DNA-Double Strand Breaks

DNA double-strand breaks (DSBs) pose a threat to cell survival and genomic integrity, and remarkable mechanisms exist to deal with these breaks. A single DSB activates a signalling response that profoundly impacts cell physiology, not least through the engagement of DSB repair pathways and the arrest of cell division. Here I study these processes in the budding yeast Saccharomyces cerevisiae and investigate two central themes to this response. First, I examine how the natural ends of chromosomes, telomeres, are differentiated from DSBs by generating DNA ends with increasing telomeric character. I discover a striking transition in the activity of the telomerase inhibitor Pif1 at these ends and propose that this is the dividing line between DSBs and telomeres. Second, I investigate a phenomenon whereby a DSB increases the mobility of chromosomes within the nucleus. This increase in mobility is dependent on the Mec1 kinase and is proposed to promote repair by homologous recombination. I identify that the Mec1-dependent phosphorylation of Cep3, a kinetochore component, is required to stimulate chromatin mobility following DNA breakage and provide a new model for how a DSB affects the constraints on chromosomes. Unexpectedly, I find that increased mobility is not required for DSB repair and instead propose that Cep3 helps arrest the cell cycle in response to a DSB. Finally, my investigation into Cep3 phosphorylation provides new insight into the role of chromatin remodelers and the histone variant H2A.Z in DSB-induced chromatin mobility.
Computer Vision Problems in 3D Plant Phenotyping

In recent years, there has been significant progress in Computer Vision based plant phenotyping (quantitative analysis of biological properties of plants) technologies. Traditional methods of plant phenotyping are destructive, manual and error prone. Due to non-invasiveness and non-contact properties as well as increased accuracy, imaging techniques are becoming state-of-the-art in plant phenotyping. Among several parameters of plant phenotyping, growth analysis is very important for biological inference. Automating the growth analysis can result in accelerating the throughput in crop production. This thesis contributes to the automation of plant growth analysis. First, we present a novel system for automated and non-invasive/non-contact plant growth measurement. We exploit the recent advancements of sophisticated robotic technologies and near infrared laser scanners to build a 3D imaging system and use state-of-the-art Computer Vision algorithms to fully automate growth measurement. We have set up a gantry robot system having 7 degrees of freedom hanging from the roof of a growth chamber. The payload is a range scanner, which can measure dense depth maps (raw 3D coordinate points in mm) on the surface of an object (the plant). The scanner can be moved around the plant to scan from different viewpoints by programming the robot with a specific trajectory. The sequence of overlapping images can be aligned to obtain a full 3D structure of the plant in raw point cloud format, which can be triangulated to obtain a smooth surface (triangular mesh), enclosing the original plant. We show the capability of the system to capture the well known diurnal pattern of plant growth computed from the surface area and volume of the plant meshes for a number of plant species. Second, we propose a technique to detect branch junctions in plant point cloud data. We demonstrate that using these junctions as feature points, the correspondence estimation can be formulated as a subgraph matching problem, and better matching results than state-of-the-art can be achieved. Also, this idea removes the requirement of a priori knowledge about rotational angles between adjacent scanning viewpoints imposed by the original registration algorithm for complex plant data. Before, this angle information had to be approximately known. Third, we present an algorithm to classify partially occluded leaves by their contours. In general, partial contour matching is a NP-hard problem. We propose a suboptimal matching solution and show that our method outperforms state-of-the-art on 3 public leaf datasets. We anticipate using this algorithm to track growing segmented leaves in our plant range data, even when a leaf becomes partially occluded by other plant matter over time. Finally, we perform some experiments to demonstrate the capability and limitations of the system and highlight the future research directions for Computer Vision based plant phenotyping.
Mechanistic impact of Enterococcus faecalis metalloprotease on bacterial virulence in the context of chronic intestinal inflammation

Endogenous proteases play an important role in the development of inflammatory bowel diseases (IBD). It is reported that Enterococcus faecalis ( E. faecalis ) triggers chronic inflammation in experimental colitis. The metalloprotease Gelatinase (GelE) is contributing to this process. It could be demonstrated that GelE impaired barrier function of intestinal epithelial cells. The extracellular domain of adherence junction protein E-Cadherin was reduced after GelE exposure. Furthermore, E-Cadherin could be directly degraded by GelE. Moreover, purified proteolytically active GelE reduced mucosal barrier function of distal colon segments from disease susceptible mice. In order to elucidate the pro-inflammatory mechanisms of E. faecalis , mutants for GelE and the enterococcal polysaccharide antigen B have been generated. Future experiments will unravel the role of commensal E. faecalis in the development of IBD.
Environmental controls on the causes and functional consequences of tree species diversity

Knowledge of the functional consequences of biodiversity is increasing through studies of both experimental systems and natural systems. Community assembly theory has also helped to reveal the causes of biodiversity organization. However, the causes and consequences of biodiversity have been discussed in parallel and simultaneous consideration of both has been limited, even though they are both influenced by regional environmental conditions. To understand the relationship between biodiversity and productivity, I focused on the linkages between the number of tree species and biomass productivity across forest biomes under a range of bioclimatic conditions. I found that high tree diversity generally increased productivity. This was primarily due to a selection process that results from a high probability of having high‐performance species and their dominance at high diversity, regardless of the biome. In less‐productive biomes, the residual importance of diversity, which likely reflects other forms of biological interactions (including species complementarity), increased productivity. These findings of differential diversity effects under different environmental conditions are consistent with the existing theory of community assembly, which predicts a shift in the assembly process from stochasticity to determinism with increasing environmental harshness. Analyses based on functional trait diversity also supported this theory: stochastic assembly (resulting in the selection effect) and deterministic assembly (possibly resulting from interspecific niche differences) became more important in productive and less‐productive biomes, respectively. Synthesis. Increasing our understanding of the causalities between diversity and other characteristics, such as productivity, is crucial, particularly for forest ecosystems, because of the increasing interest in productivity‐related ecosystem services supported by diverse assemblages of trees.
Juvenile Penaeid Shrimp Ecology in a Louisiana Coastal Marsh Management Area.

Juvenile penaeid shrimp were studied by a variety of methods in a southwest Louisiana, brackish marsh. Most of the work was conducted in two study ponds, one with a fixed-crest weir and the other without. In mark and recapture studies, both brown shrimp Penaeus aztecus and white shrimp P. setiferus were found to grow faster in marsh behind a fixed-crest weir. There was no apparent weir effect on mortality of either species. Brown shrimp emigrated an average of 12 d later from marsh behind the weir; white shrimp were sometimes delayed by the weir. The peak of brown shrimp emigration from both weired and unweired marsh peaked coincided with both new and full moons. I used four methods of estimating juvenile shrimp standing stocks and found that shrimp were usually less abundant in the weired than the unweired pond. The reduction in observed emigration of shrimp from a weired area was likely caused by restricted immigration past the weir. I used density estimates from the unweired study pond and a nearby marsh pond to confirm that export estimates in previous studies of the unweired pond were reasonable, although conservative, estimates of normal numbers of shrimp emigrating from similar marsh ponds. Graphic analysis, linear statistics, and superposed epoch analysis were used to study effects of environmental variables on white shrimp emigration. White shrimp emgration from the marsh was associated with decreasing temperatures, high water outflow, decreasing and/or low barometric pressure, and rainfall. TABLE OF CONTENTS Acknowledgments . ii Abstract. iii CHAPTER
TÜRKİYE VE KKTC TÜKETİCİLERİNİN DEMOGRAFİK ÖZELLİKLER AÇISINDAN ETNOSENTRİZM DÜZEYLERİNİN İNCELENMESİNE YÖNELİK BİR KARŞILAŞTIRMA

Tuketici davranislari, pazarlama literaturunde daima ilgi ceken ve arastirilan bir alandir. Pazarlamanin dinamik yapisinin bir sonucu olarak bu genis alanda da, surekli yeni kavramlar gelismekte ve arastirmacilarin dikkatlerini cekmektedir. Son zamanlarda ozellikle Avrupa ve Amerika’da ilgi goren bu yeni kavramlardan biri de “tuketici etnosentrizmi”dir. 90’li yillarin baslarinda literature girmesine ragmen cok kisa bir zamanda tuketici etnosentrizmi farkli acilardan pek cok arastirmaya konu olmayi basarmistir. Ancak Turkiye’de bu kavramin yurt disindaki kadar cabuk beiiimsenemedigi ve yapilan calismalarin sinirli sayida oldugu gorulmektedir. Bu calisma, literature bu baglamda katki saglamayi amaclamaktadir. Calismada ilk olarak etnosentrizmi, tuketici etnosentrizmi ve tuketici etnosentrizminin olculmesi kavramlari Incelenmektedir. Metodoloji bolumunde ise Turkiye, daha once bu konuda hicbir calisma yapilmamis olan Kuzey Kibris Turk Cumhuriyeti ile tuketici etnosentrizmi duzeyleri ve demografik degiskenlerin bu duzeyler uzerindeki etkilerinin benzer olup olmamasi acisindan karsilastirilmaktadir. Tuketici etnosentrizm duzeyinin olculmesinde ise pek cok arastirmada gecerliligi ve guvenilirligi ispat edilmis olan CETSCALE kullanilmistir.
Dietary Chromium Supplementation for Pigs and Chickens.

Three experiments were conducted with pigs and four experiments were conducted with chickens to determine the effects of supplemental dietary Cr on growth performance, carcass characteristics, tissue minerals and plasma metabolite and hormone concentrations. In pigs (Exp. 1) 200 ppb Cr from seven different sources tended to decrease growth performance during the grower phase and increase growth performance during the finisher phase. Dietary Cr had minimal effects on plasma metabolite and hormone concentrations and Cr did not affect carcass characteristics. In general, dietary Cr increased tissue Cr concentration, except for longissimus muscle (LM). In Exp. 2, pigs were fed 400 ppb Cr as Cr chloride, Cr nicotmate, or Cr picolinate (CrPic) to determine the effect of these Cr sources on i.v. glucose tolerance and insulin sensitivity. None of the Cr sources affected glucose clearance rate or half-life, or insulin clearance rate or half-life. In Exp. 3, the interactive effects of two levels o f dietary lysine, two levels of dietary Cr, and two levels of pen space were evaluated. During the finisher phase, Cr increased average daily gain and gain/feed o f pigs fed 80% of the lysine requirement but not in pigs fed 120% of the lysine requirement. In addition, Cr decreased tenth rib fat thickness (TRF) in pigs given adequate pen space but increased TRF of pigs given inadequate pen space. Dietary Cr supplementation did not affect LM area. Three experiments were conducted to determine the effect of CrPic on growth performance, plasma metabolites and hormones, and carcass composition of
Global connectivity of the frontoparietal cognitive control network is related to depression symptoms in undiagnosed individuals

We all vary in our mental health, even among healthy (undiagnosed) individuals. Understanding this variability may reveal factors driving the onset of mental illness, as well as factors driving sub-clinical mental health problems that can still influence quality of life. To better understand the large-scale brain network mechanisms underlying this variability in mental health we examined the relationship between mental health symptoms and resting-state functional connectivity patterns in cognitive control systems. The frontoparietal cognitive control network (FPN) consists of flexible hubs that can regulate distributed systems depending on current goals, and dysfunction in the FPN has been identified in a variety of psychiatric disorders. Alterations in FPN connectivity may influence mental health by disrupting the ability to regulate symptoms in a goal-directed manner. This suggests that the FPN may play an important role in the promotion and maintenance of mental health generally. Here we test the hypothesis that disruptions in FPN connectivity are related to mental health (depression) symptoms even among healthy individuals. This hypothesis is consistent with a general role of FPN in the regulation of mental health symptoms. We found that depression symptoms were negatively correlated with between-network global connectivity (BGC) of the FPN as well as the default mode network (DMN). This suggests that decreased connectivity between the FPN (and, separately, DMN) and the rest of the brain is related to increased depression symptoms among undiagnosed individuals. These findings complement previous clinical studies to support the hypothesis that global FPN connectivity contributes to the regulation of mental health symptoms across both mentally healthy and unhealthy individuals.
Performance of an Ambulatory DRY-EEG Device for Auditory Closed-Loop Stimulations in the Home Environment

Objective Recent research has shown that auditory closed-loop stimulations can enhance sleep slow oscillations (SO) to improve N3 sleep quality and cognition. Previous studies have been conducted in a lab environment and on a small sample size. The present study aimed at validating and assessing the performance of a novel ambulatory wireless dry-EEG device (WDD), for auditory closed-loop stimulations of SO during N3 sleep at home. Material and Methods The performance of the WDD to detect N3 sleep automatically and to send auditory closed-loop stimulations on SO were tested on 20 young healthy subjects who slept with both the WDD and a miniaturized polysomnography (part 1) in both stimulated and sham nights within a double blind, randomized and crossover design. The electrophysiological effects of auditory closed-loop stimulation on delta power increase were assessed after 1 and 10 nights of stimulations on an observational pilot study in the home environment including 90 middle-aged subjects (part 2). Results The sensitivity and specificity of the WDD to automatically detect N3 sleep in real-time were 0.70 and 0.90, respectively. The stimulation accuracy of the SO ascending-phase targeting was 45±52°. The stimulation protocol induced an increase of 39.5 % of delta power after the stimulations. The increase of SO response to auditory stimulations remained at the same level after 10 consecutive nights. Conclusion The WDD shows good performances to automatically detect in real-time N3 sleep and to send auditory closed-loop stimulations on SO accurately. These stimulations increased the SO amplitude during N3 sleep without any adaptation effect after 10 consecutive nights. This tool provides new perspectives to figure out novel sleep EEG biomarkers in longitudinal studies and can be interesting to conduct broad studies on the effects of auditory stimulations during sleep.