Miracle-dz/UniFAR-FTUs huggingface dataset:
Development of InDel marker for rice blast resistance gene Pi9

Pi9 is one of the major blast resistance genes which encodes a nucleotide-binding site-leucine-rich repeat (NBS-LRR) domain-containing protein. This gene was observed to show resistance against many pathotypes of the blast pathogen in Malaysia. Resistance allele Pi9 from rice variety 75-1-127 had previously been cloned using map-based cloning strategy. The gene sequence was used to design specific primers to amplify susceptible Pi9 allele from MR219 rice variety prior to cloning. The resistance and susceptible allele of Pi9 were 8.587kb and 8.785kb in length respectively. Allele mining was carried out by comparing between the susceptible and resistance allele of Pi9. One potential InDels polymorphism at position 590bp and 920bp was identified. Primer named as Pi9_InDel was designed targeting this region in such a way that the resistance and susceptible genotypes yielded 327 bp and 438 bp amplicon respectively.
Genotyping of Toxoplasma gondii Isolated from Aborted Iraqi Women

Background: Toxoplasmosis is a worldwide-distributed infection which is mostly asymptomatic but can cause serious health problems in congenitally-infected newborns. Objectives: Genotyping of Toxoplasma gondii and its distribution among aborted Iraqi pregnant and its relationship with sero-prevalence of alpha-fetoprotein positivity among toxoplasmosis cases. Martials and Methods: Ninety six blood and amniotic fluids samples were collected from aborted women that are suspected to have Toxoplasma gondii infection from 368 samples collected from Al-Sadir Hospital, Al-Habibia Hospital, Al-Ilwea Hospital, Baghdad for delivery Hospital, Al Khark Hospital, and Educational Laboratories of medicine City, during the period from the 1 st May 2014 till the end of June 2015.The results of aborted women investigations were compared with those of 79 apparently healthy controls volunteers pregnant. Results: This study revealed that there is a highly significant increment in genotyping of Toxoplasma Type II, [9(15.25%)], type I and III [2(3.38)]. While the distribution the genotypes of Toxoplasma strains according to age groups showed that the highest frequency (55.6%) of Type I was among those at age (15-25) years, while Type II was predominant (39.6%) among the age group (36-45) years. For Type III, it was observed in very low percentage among aborted (only 2 cases out of 96). The results showed a highly significant difference in IgM level [48(93.8%)] among type II, [9(100%)] Type I, and [2(100%)] Type III in comparison with healthy control (P<0.01). Moreover, the current results revealed a highly significant different in Alpha-fetoprotein AFP positivity among [8(88.9 % )], [46(95.8%)] and [2(100.0%)] for Type 1, II and III respectively in comparison with [16(43.2%)] of healthy control While level of AFP (P<0.01). Conclusions: In view of the current results it could be concluded that type II strain was the most common strain among the Genotypes. The genotype I the most deadly type, while type III, which is an entero-zoonotic parasite recorded for the first time in Iraq.
GROWTH ANALYSIS OF AREA, PRODUCTION AND PRODUCTIVITY OF WHEAT CROP IN HARYANA AND INDIA

The study intends to scrutinize the performance of wheat production in Haryana and India during the period 1966-67 to 2012-13; this time period were divided in five sub periods i.e. P-I (1966-67 to 197576), P-II (1976-77 to 1985-86), P-III (1986-87 to 1995-96), P-IV (1996-97 to 2005-06) and P-V (200607 to 2012-13). The study is exclusively based on secondary data. The Result of study revealed positive trends in area, production and yield of wheat for both Haryana and India. Similar results were obtained on the triennium basis. The contribution of area and yield in the production of wheat are comparable for both Haryana and India. All the selected three aspects (i.e. area, production and yield) have shown positive growth rates in Haryana while in case of India, positive growth rates were observed for only area and production except in PeriodIV (1996-97 to 2005-06). Trend of yield in India was similar to that of Haryana. Similar results are observed for coefficient of variation and stability indices in production and yield of wheat in Haryana as well as India. * Corresponding author KEYWORDS
Estudos filogenéticos moleculares e taxonômicos na subtribo Arthrostylidiinae (Poaceae: Bambusoideae: Bambuseae)

xi INTRODUÇÃO GERAL . 1 REFERÊNCIAS BIBLIOGRÁFICAS . 5 CAPÍTULO I: MOLECULAR PHYLOGENETICS OF AULONEMIA AND COLANTHELIA (POACEAE: BAMBUSOIDEAE: BAMBUSEAE: ARTHROSTYLIDIINAE) BASED ON MULTI-LOCUS PLASTID SEQUENCES . 8 ABSTRACT . 9. 9 RESUMO . 9 INTRODUCTION . 11 MATERIAL AND METHODS . 14 RESULTS. 16 DISCUSSION. 19 ACKNOWLEDGMENTS. 25 LITERATURE CITED. 25 TABLES. 31 FIGURES . 38 APPENDIX . 42 CAPÍTULO II: COLANTHELIA LONGIPETIOLATA (POACEAE: BAMBUSOIDEAE), A NEW SPECIES OF WOODY BAMBOO FROM THE BRAZILIAN ATLANTIC FOREST. 46 ABSTRACT . 47. 47 RESUMO . 47 INDRODUCTION. 48 MATERIAL AND METHODS . 48 TAXONOMIC TREATMENT . 49 ACKNOWLEDGMENTS. 53
On the complexity of mod-2l sum PLA's

Consideration is given to the realization of logic functions by using PLAs with an exclusive-OR (EXOR) array, where a function is represented by mod-2 (EXOR) sum-of-products (ESOPs) and both true and complemented variables are used. The authors propose a new PLA structure using an EXOR array. They derive upper bounds on the number of products of this type of PLA that are useful for estimating the size of a PLA as well as for assessing the minimality of the solutions obtained by heuristic ESOP minimization algorithms. Computer simulation using randomly generated functions shows that PLAs with the EXOR array require, on the average, fewer products than conventional PLAs. For symmetric functions, the authors conjecture that the PLAs with an EXOR array require, at most, as many products as the conventional PLAs. The proposed PLAs can be made easily testable by adding a small amount of hardware. >
Optogenetic characterization of corticotropin-releasing factor pathways in the central nucleus of the amygdala in alcohol dependence

In alcohol-dependent animals, withdrawal from alcohol activates a neuronal ensemble in the central nucleus of the amygdala (CeA) that is responsible for the escalation of alcohol drinking. However, the neuronal phenotype and neuronal pathways that are controlled by these neurons are unknown. We investigated the cellular identity of this CeA neuronal ensemble and found that most neurons expressed corticotropin-releasing factor (CRF). Using Crh -Cre transgenic rats combined with in vivo optogenetics, we tested whether the inactivation of CeA CRF neurons prevents excessive alcohol self-administration during withdrawal. Rats were injected with AAV-DIO-NpHR-eYFP or AAV-DIO-eYFP (control) and implanted with optical fibers in the CeA. The animals were then exposed to chronic intermittent ethanol to induce alcohol dependence. The inactivation of CeA CRF neurons decreased alcohol drinking in dependent rats to levels that were observed before the animals became dependent and completely prevented activation of the entire CeA neuronal ensemble (Fos+ neurons) during withdrawal. No effect was observed in the AAV-DIO-eYFP control group or on water or saccharin self-administration in either group. In a second experiment, the rats were injected with AAV-DIO-NpHR-eYFP in the CeA, and optical fibers were implanted into downstream projection regions of CeA CRF neurons, including the bed nucleus of the stria terminalis (BNST), lateral hypothalamus (LH), parasubthalamic nucleus (pSTN), substantia innominata (SI), and parabrachial nuclei (PBN). The optogenetic inactivation of CRF terminals in the BNST recapitulated the effect on alcohol drinking that was observed with the inactivation of CeA CRF cell bodies, whereas inactivation of the LH, SI, and PBN had no effect. These results indicate that the activation of CeA CRF neurons during withdrawal is required for recruitment of the CeA neuronal ensemble that is responsible for excessive alcohol drinking in dependent rats. The CRF projection to the BNST but not LH, pSTN, SI, test with in vivo optogenetics and immediate early gene brain mapping. dissected the role of the different downstream CeA-CRF pathways in alcohol dependence using optogenetic inactivation of CRF terminals from CeA neurons that project to the BNST (CRF CeA-BNST LH and pSTN CeA-LH/pSTN substantia innominata (SI; CRF CeA-SI and parabrachial CRF CeA-PBN ; self-administration, F 1,14 p F 2,28 no ´ F medial amygdala (CeM), and central amygdala (CeC). The optogenetic inhibition of CeL CRF neurons
The probability distribution of the reconstructed phylogenetic tree with occurrence data

We consider a homogeneous birth-death process with incomplete sampling. Three successive sampling schemes are considered. First, individuals can be sampled through time and included in the tree. Second, they can be occurrences which are sampled through time and not included in the tree. Third, individuals reaching present day can be sampled and included in the tree. Upon sampling, individuals are removed (i.e. die). The outcome of the process is thus composed of the reconstructed evolutionary tree spanning all individuals sampled and included in the tree, and a timeline of occurrence events which are not placed along the tree. We derive a formula allowing one to compute the joint probability density of these, which can readily be used to perform maximum likelihood or Bayesian estimation of the parameters of the model. In the context of epidemiology, our probability density allows us to estimate transmission rates through a joint analysis of epidemiological case count data and phylogenetic trees reconstructed from pathogen sequences. Within macroevolution, our equations are the basis for taking into account fossil occurrences from paleontological databases together with extant species phylogenies for estimating speciation and extinction rates. Thus, we provide the theoretical framework for bridging not only the gap between phylogenetics and epidemiology, but also the gap between phylogenetics and paleontology.
ESTIMATING THE CRITICAL ASSESSMENT GAP FROM TRAFFIC MOVEMENTS

At unsignalised intersections, when making opposed turns at signalised intersections, when overtaking on two lane rural roads, drivers are assumed to be waiting for an acceptable gap before moving. This minimum acceptable gap for a particular driver is termed his critical gap. A driver population is usually represented by the mean critical gap which is termed the critical acceptance gap and is then used in the appropriate formula to estimate capacity and delay. This report is to document the techniques to be used to estimate the parameters for drivers' critical gaps using the maximum likelihood technique. (A)
Neoproterozoic origin and multiple transitions to macroscopic growth in green seaweeds

Significance Green seaweeds are important primary producers along coastlines worldwide. Their diversification played a key role in the evolution of animals. To understand their origin and diversification, we resolve key relationships among extant green algae using a phylotranscriptomic approach. A time-calibrated tree, inferred from available fossil data, reconstructs important evolutionary events, such as transitions to benthic environments and the evolution of macroscopic growth in the late Tonian/Cryogenian periods, followed by a marked Ordovician diversification of macroscopic forms. This ancient proliferation of green seaweeds likely modified shallow marine ecosystems, which set off an evolutionary arms race between ever larger seaweeds and grazers. The Neoproterozoic Era records the transition from a largely bacterial to a predominantly eukaryotic phototrophic world, creating the foundation for the complex benthic ecosystems that have sustained Metazoa from the Ediacaran Period onward. This study focuses on the evolutionary origins of green seaweeds, which play an important ecological role in the benthos of modern sunlit oceans and likely played a crucial part in the evolution of early animals by structuring benthic habitats and providing novel niches. By applying a phylogenomic approach, we resolve deep relationships of the core Chlorophyta (Ulvophyceae or green seaweeds, and freshwater or terrestrial Chlorophyceae and Trebouxiophyceae) and unveil a rapid radiation of Chlorophyceae and the principal lineages of the Ulvophyceae late in the Neoproterozoic Era. Our time-calibrated tree points to an origin and early diversification of green seaweeds in the late Tonian and Cryogenian periods, an interval marked by two global glaciations with strong consequent changes in the amount of available marine benthic habitat. We hypothesize that unicellular and simple multicellular ancestors of green seaweeds survived these extreme climate events in isolated refugia, and diversified in benthic environments that became increasingly available as ice retreated. An increased supply of nutrients and biotic interactions, such as grazing pressure, likely triggered the independent evolution of macroscopic growth via different strategies, including true multicellularity, and multiple types of giant-celled forms.
Norwegian dairy farmers’ preferences for breeding goal traits and associations with herd and farm characteristics

ABSTRACT The aims of this study were to investigate variation and clustering in breeding goal trait preferences among Norwegian dairy farmers and to identify factors with a systematic influence on their preferences. An internet-based questionnaire was sent out to dairy farmers connected to the Norwegian co-operative breeding organization Geno (N = 8222), of which 10.8% answered (N = 888). Of the 15 suggested traits fertility had the highest overall ranking, while parasite resistance and methane emission had the lowest. Four distinct preference clusters were identified by the means of cluster analysis, of which two had a high preference for milk production. Differences in terms of farm and herd characteristics between clusters suggests a mixture of systematic and intrinsic effects on breeding goal trait priorities. This study shows that Norwegian dairy farmers’ preferences for breeding goal traits fall into four distinct clusters, both affected by herd and farm characteristics along with intrinsic values.
The productivity of mixed mountain forests comprised of Fagus sylvatica, Picea abies, and Abies alba across Europe

Mixed mountain forests of European beech (Fagus sylvatica L.), Norway spruce (Picea abies (L.) Karst), and silver fir (Abies alba Mill.) cover a total area of more than 10 million hectares in Europe. Due to altitudinal zoning, these forests are particularly vulnerable to climate change. However, as little is known about the long-term development of the productivity and the adaptation and mitigation potential of these forest systems in Europe, reliable information on productivity is required for sustainable forest management. Using generalized additive mixed models this study investigated 60 long-term experimental plots and provides information about the productivity of mixed mountain forests across a variety of European mountain areas in a standardized way for the first time. The average periodic annual volume increment (PAI) of these forests amounts to 9.3 m3ha−1y−1. Despite a significant increase in annual mean temperature the PAI has not changed significantly over the last 30 years. However, at the species level, we found significant changes in the growth dynamics. While beech had a PAI of 8.2 m3ha−1y−1 over the entire period (1980–2010), the PAI of spruce dropped significantly from 14.2 to 10.8 m3ha−1y−1, and the PAI of fir rose significantly from 7.2 to 11.3 m3ha−1y−1. Consequently, we observed stable stand volume increments in relation to climate change.
TLX3 repressed SNAI1-induced epithelial-mesenchymal transition by directly constraining STAT3 phosphorylation and functionally sensitized 5-FU chemotherapy in hepatocellular carcinoma

TLX3 has an established role as a sequence-specific transcription factor with vital functions in the nervous system. Although several studies have shown that TLX3 is aberrantly up-regulated in leukemia, its expression and function in hepatocellular carcinoma (HCC) remain unknown. We found that TLX3 expression was decreased in 68/100 (68%) HCC cases and negatively correlated with the expression of p-STAT3, SNAI1, and Vimentin, while it was positively associated with E-cadherin expression. ITRAQ proteomic profiling revealed significantly less TLX3 expression in primary HCC tumors than in portal vein tumor thrombi. Comparison of Kaplan-Meier curves showed that down-regulation of TLX3 in HCC was associated with poor post-surgical survival. TLX3 over-expression inhibited HCC cell viability, proliferation, migration, invasion and enhanced 5-FU treatment, whereas silencing TLX3 produced the opposite results. Further experiments showed that TLX3 attenuated the EMT phenotype. In vivo experiments showed that knockdown of TLX3 promoted the growth of HCC xenografts and attenuated the anti-tumor effects of 5-FU treatment. Gene expression microarray analysis revealed that TLX3 inhibited IL-6/STAT3 signaling. In additional mechanistic studies TLX3 reversed the EMT phenotype of HCC cells by binding to STAT3, inhibiting STAT3 phosphorylation, and down-regulating SNAI1 expression. Taken together, loss of expression of TLX3 induces EMT by enhancing IL-6/STAT3/SNAI1 signaling, and accelerates HCC progression while also attenuated the effect of 5-FU on HCCs.
Base-rate neglect and neural computations for subjective weight in probabilistic inference

Humans show systematic biases when estimating probability of uncertain events. Base-rate neglect is a well-known bias that describes the tendency to underweight information from the past relative to the present. In this study, we characterized base-rate neglect at the computational and neural implementation levels. At the computational level, we established that base-rate neglect arises from insufficient adjustment to weighting prior information in response to changes in prior variability. At the neural implementation level, we found that orbitofrontal cortex (OFC) and medial prefrontal cortex (mPFC) represent subjective weighting of information that reflects base-rate neglect. Critically, both subjective-weight and subjective-value signals that guide choice were found in mPFC. However, subjective-weight signals preceded subjective-value signals. These results indicate that when facing multiple sources of information, estimation bias such as base-rate neglect arises from information weighting computed in OFC and mPFC, which directly contributes to subjective-value computations that guide decisions under uncertainty. Significance Statement Facing uncertainty, estimating the probability of different potential outcomes carries significant weight in affecting how we act and decide. Decades of research show that humans are prone to giving biased estimation but it remains elusive how these biases arise in the brain. We focus on base-rate neglect, a well-known bias in probability estimation and find that it is tightly associated with activity in the medial prefrontal cortex and orbitofrontal cortex. These regions represent the degree to which human participants weigh different sources of information, suggesting that base-rate neglect arises from information-weighting computations in the brain. As technology provides us the opportunity to seek and gather information at an ever-increasing pace, understanding information-weighting and its biases also carry important policy implications.
Sex ratio and sex expression in an urban population of the silver moss, Bryum argenteum Hedw.

ABSTRACT Introduction. A well-supported pattern among dioicous bryophytes is male rarity. However, few assessments of bryophyte sex ratios have been made across environmental gradients to assess the role of environment in shaping population sex ratios. Methods. We systematically surveyed 200 shoots from a 20 m2 urban population of Bryum argenteum, and regenerated each shoot apex until sex expression occurred (up to 315 days). Key results. Female shoots outnumbered male shoots 132 to 68, giving a sex ratio of 1.94♀: 1♂. The female bias was found in two transects in higher light environments but not in the third transect, which had a lower light level and an equal sex ratio. Female shoots took longer than male shoots to reach gametangial induction (122 vs. 60 days) and longer to produce 5 inflorescences (120 vs. 80 days). Male shoots produced an average of 10× the total number of inflorescences compared to female shoots (34 vs. 3.5 inflorescences). Despite producing more inflorescences, male plants also produced more regenerant shoots, thus contradicting the prediction that a higher prefertilisation reproductive effort in males trades off with vegetative proliferation. Female plants harboured significantly more associated microbes than male plants. Conclusions. Our results support the role of light in influencing sex ratios in this species, suggest that trade-offs between reproduction and vegetative growth may not be strong for males, and indicate a potential role of a sex-specific microbiome in influencing sex ratios.
The role of the human nasal cavity in patterns of craniofacial covariation and integration

Climate has a selective influence on nasal cavity morphology. Due to the constraints of cranial integration, naturally selected changes in one structure necessitate changes in others in order to maintain structural and functional cohesion. The relationships between climate and skull/nasal cavity morphology have been explored, but the integrative role of nasal variability within the skull as a whole has not. This thesis presents two hypotheses: 1) patterns of craniofacial integration observed in 2D can be reproduced using 3D geometric morphometric techniques; 2) the nasal cavity exhibits a higher level of covariation with the lateral cranial base than with other parts of the skull, since differences in nasal morphology and basicranial breadth have both been linked to climatic variables. The results support the former hypothesis, but not the latter; covariation observed between the nasal cavity and other cranial modules may suggest that these relationships are characterized by a unique integrative relationship.