Miracle-dz/UniFAR-FTUs huggingface dataset:
Nucleotide sequence changes in the MSX1 and IRF6 genes in Lithuanian patients with nonsyndromic orofacial clefting

Department of Human and Medical Genetics, Faculty of Medicine, Vilnius University, Vilnius, Lithuania Background. Nonsyndromic orofacial clefing (NS-OFC) is among the most common malformations in humans. It is a complex multifactorial trait with a considerable genetic component. Among numerous candidate genes, those related to syndromic OFC recently have emerged as particularly strong ones. Our study was aimed to investigate whether mutations in the MSX1 and IRF6 genes contribute to NS-OFC in the population of Lithuania. Patients, materials and methods. Patients with NS-OFCs from Lithuania were tested for nucleotide sequence changes in the MSX1 gene (80 patients) and IRF6 gene (190 patients). DNA fragments covering MSX1 gene and exonic parts of the IRF6 gene were PCR-amplified, and the direct sequencing of the PCR products was performed with a subsequent comparison of sequencing results with reference DNA sequences of the genes. Results. Eight and 22 different nucleotide sequence changes were revealed in the MSX1 and IRF6 genes, respectively. While only already known functionally neutral polymorphisms were detected in the MSX1 gene, scanning IRF6 gene resulted in nine novel nucleotide sequence variants. Of them, three were missense mutations (p.S212I, p.L295P, p.R400L), which, together with the p.A61G mutation found in the case of Van der Woude syndrome, might be related to the NS-OFC phenotype in the population of Lithuania. Conclusions. Failure to find MSX1 gene mutations potentially related to NS-OFC phenotype of the probands from Lithuania does not reject the necessity to continue investigation on a larger population sample. Our study highlights the IRF6 gene sequence variability and supports the hypothesis that variation in this gene contributes to NS-OFC phenotype, encouraging further investigations to test whether IRF6 gene mutations identified in individuals from Lithuania are rare alleles causative for NS-OFC.
Reciprocal effects and selection for altered fatty acid composition of soybean oil

GILSINGER, JESSE JOHN. Reciprocal Effects and Selection for Altered Fatty Acid Composition of Soybean Oil. (Under the direction of Joseph W. Burton.) This study focused on altered fatty acid content of soybean oil and consisted of three objectives: (1) to study maternal effects for fatty acid composition , (2) to study reciprocal effects for heritability and stability of increased oleic acid content, and (3) to examine how other traits are affected by selection for increased oleic acid content. Maternal effects were evaluated in 2005, 2006, and 2007 by analyzing reciprocal F1 seed resulting from crosses between the mid-oleic line N98-4445A and Dare, Haberlandt, Ogden, Arksoy, Midwest, and Peking. Reciprocal F1 seeds from a cross between the increased palmitic line N02-4441 and Dare were grown in vitro. The results showed that maternal effects for fatty acid composition were significant across a wide range of genetic materials and environments. Maternal effects for the F1 seed dissipated while differences between parents were maintained when grown in vitro. Reciprocal effects for heritability and stability were examined in twelve F2 derived populations over two years developed from reciprocal crosses between N98-4445A and Arksoy, Dare, Haberlandt, Midwest, Ogden, and Peking. Significant differences in heritability and stability between reciprocal populations were observed, suggesting it may be advantageous to make reciprocal crosses when developing populations for altered fatty acid selection in soybeans. To investigate selection for increased oleic acid content, two populations consisting of approximately 60 F4:6 lines were generated by crossing N98-4445A with the cultivars Dare and Tracy and planted as replicated trials at two North Carolina locations in 2006. Fatty acid composition, height, lodging, seed size, seed quality, yield, and maturity were measured for each plot. Plants were also genotyped with SSR markers. An increase in oleic acid was correlated with a decrease in yield and seed quality. Significant marker-trait associations for oleic acid content, seed quality, and yield were observed in both populations. These results demonstrate that these markers could be useful for marker-assisted selection for the mid-oleic trait across populations and could be used to improve seed quality and yield. Reciprocal Effects and Selection for Altered Fatty Acid Composition of Soybean Oil by Jesse John Gilsinger A dissertation submitted to the Graduate Faculty of North Carolina State University In partial fulfillment of the Requirements for the Degree of Doctor of Philosophy Crop Science Raleigh, North Carolina
Nonreciprocal Hybridization Failure in Crosses between Annual Wild-Rice Species (Zizania palustris X Z. aquatica: Poaceae)

Natural interspecific hybridization has been proposed to account for morphological variation in the annual members of the genus Zizania, commonly known as wild-rice, although isozyme data, as reported in a single study, have disclosed no evidence of introgression. Experimental hybridizations were conducted in all possible combinations among the five varieties of the two annual species of wild-rice. Meaningful intraspecific variation in crossability was not detected, which is in agreement with morphological and isozyme data. A unilateral interspecific crossability barrier was found between the two annual species. Pistillate florets of Z. palustris typically failed to produce viable fruits when pollinated by Z. aquatica. The reciprocal interspecific cross was successful at a low level of crossability. This evidence further strengthens the taxonomic separation of the two annual species previously defined by spikelet morphology, ultrastructure, and isozyme varia- tion. Examination of pollinated stigmas of the infertile types of crosses disclosed that pollen tubes had penetrated the entire length of the stigma. The crossing barrier is therefore not due to a pollen/ stigma interaction that severely interferes with pollen tube growth. Interspecific F, hybrids ex- pressed the spikelet morphology of the Z. aquatica parent exclusively, although other morphological characters were typically expressed as intermediate to those of the parent species. The potential for natural hybridization between Z. aquatica and Z. palustris is discussed.
Research on the Robust and Low-cost Computer Method Based on Deep Residual Learning

At this exact moment on our planet, there's are more than 65.2 million people suffering from visual illnesses caused by cataract. It is the cause of a third of all blindness in the world, and 99% of these patients live in developing countries. However the recovery surgery is one of the most cost-effective ones in the field. Lack of medical care is the real cause of such skyrocketing number of patients in developing country. Out of this reason, I developed an integrated diagnosis system based on deep learning methods, which could diagnose cataract with the accuracy of 91.7%. The high accuracy and the low-cost features of this diagnosis method make it an excellent auxiliary tool of preliminary diagnosis in developing countries. The best performance is held by the 50-layer deep residual neural network trained with Adam optimizer, which could adjust learning rate according to the training status and specific weights. The further experiments with the quantity of data as a variable indicated that the best performance of deeper model is limited by the insufficient data.
A kinematic formalism for tracking ice–ocean mass exchange on the Earth's surface and estimating sea-level change

Abstract. Polar ice sheets are important components of the Earth system. As the geometries of land, ocean and ice sheets evolve, they must be consistently captured within the lexicon of geodesy. Understanding the interplay between the processes such as ice-sheet dynamics, solid-Earth deformation, and sea-level adjustment requires both geodetically consistent and mass-conserving descriptions of evolving land and ocean domains, grounded ice sheets and floating ice shelves, and their respective interfaces. Here we present mathematical descriptions of a generic level set that can be used to track both the grounding lines and coastlines, in light of ice–ocean mass exchange and complex feedbacks from the solid Earth and sea level. We next present a unified method to accurately compute the sea-level contribution of evolving ice sheets based on the change in ice thickness, bedrock elevation and mean sea level caused by any geophysical processes. Our formalism can be applied to arbitrary geometries and at all timescales. While it can be used for applications with modeling, observations and the combination of two, it is best suited for Earth system models, comprising ice sheets, solid Earth and sea level, that seek to conserve mass.
Rolling and sliding of a rigid cylinder along the boundary of a rigid-plastic half-space

A numerical solution is obtained for the problem of steady-state plane plastic flow of a rigid-plastic half-space along the boundary of which a smooth or rough rigid cylinder is rolling and sliding. The change in the shape of the plastic region and the contact arc is shown as depending on the force and torque applied to the cylinder. The limiting values of the contact arc that allow steady-state plastic flow are determined as depending on the magnitude and direction of the shear stresses due to contact friction. This problem is of interest for the theory of rolling friction and the technology of surface plastic deformation of materials by means of rolling and drawing.
New Montane Ptomaphagus Beetles from New Mexico and Zoogeography of Southwestern Caves (Coleoptera; Leiodidae; Catopinae)

Ptomaphagus lincolnensis and Ptomaphagus manzano, small-eyed, flightless, high elevation forest litter species from New Mexican mountains, are described as new. Their relation to cave species is possible. High elevation spruce-fir forests of New Mexico harbor a suite of terrestrial litter arthropods "preadapted" for cave colonization. That cave faunas in the southwest (west of the Edwards Plateau of Texas) are comparatively lacking in troglobites (obligate cavernicoles) must thus be due to environmental dryness, and not to a lack of ancestral species with cave colonizing potential and ability. Although many new species of Ptomaphagus continue to be found in Mexico and other Central American countries (Peck 1977), no new, valid, non-cavernicolous species has been found in the rest of North America since Jeannel described P. brevior in 1949 (Peck 1973). The discovery of two new species in New Mexico is thus of some interest in itself, and for their implications on the origin and evolution of cavernicolous species in the southwestern United States. All methods and terminology used in this paper follow those used in my previous revisions (Peck 1973, 1977). Trapping methods are described by Newton and Peck (1975). Paratype specimens will be distributed to collections cited in Peck (1973). Types are deposited in the Canadian National Collection of Insects (CNC), Ottawa. Ptomahagus lincolnensis new secies Holotype female and allotype male in CNC. Type locality: New Mexico, Lincoln County, Monjeau Lookout, 9000 feet elevation, about 10 miles NNW of Ruidoso, 16.viii. 1975, S. Peck, under large boulders embedded in spruce-fir forest. Paratypes: 52 with above data, and the
Effects of Nitroxin and Nitrogen Fertilizers on Grain Yield and Essential Oil from Seeds of (Anethum graveolens L.).

Aims: Dill (Anethum graveolens L.) is a perennial herbaceous plant belonging to the (Apiaceae or Umbelliferae) family, with high essential oil content, and dill leaves and and seeds are used as seasoning. This study was conducted in 2011 and 2012 at Iran County, aiming to determine the effects of biological and chemical nitrogen fertilizers on grain yield, essential oil yield, and essential oil composition of dill. Methodology: The treatments included Nitroxin bio-fertilizer (0% and 100%), and nitrogen (0, and 100 kg ha (NH4NO3)), 50% nitroxin×50 kg hanitrogen and control. A completely randomized block design with four replications was adopted. Results: Results showed highest essential oil content detected in biological fertilizer and chemical fertilizer. Identification of essential oil composition showed that content of carvone increased with application of Nitroxin biofertilizers. Conclusion: Results indicated, application of Nitroxin biofertilizers enhanced yield and essential oil content in this plant.
Molecular cloning of a C. elegans longevity gene pnc-1 and investigation of its novel function in development

The egg-laying apparatus in C. elegans is a great model system to study morphogenesis and organogenesis in developmental biology. Egg-laying defective (Egl) mutants provide powerful genetic tools to address these issues. ku212 was isolated as an allele with egg laying and associated connection of gonad defective (Cog) phenotypes. The corresponding gene was named cog-3. In this study, phenotypic analyses of ku212 revealed no obvious connection between the vulval and the uterine lumens at the appropriate stage, due to a temporal delay in uterine development. Mild delay in global gonadogenesis relative to development of extra-gonadal tissues results in the lack of temporal synchronization between the vulva and the uterus. ku212 mutants also have a specific uterine fate defect. In wild-type animals, four outer ventral uterine π cells express LET-23 EGF receptor and adopt the uterine vulval 1 (uv1) fate in response to a vulval-derived LIN-3 EGF signal. In ku212 mutants, these four uv1 cells undergo necrosis prior to full differentiation. Transformation rescue by pnc-1 and further identification of a nonsense mutation in pnc-1 in ku212 animals confirm that ku212 is an allele of pnc-1, a homolog of a yeast longevity gene Pnc1. pnc-1 encodes a nicotinamidase which converts nicotinamide (NAM) to nicotinic acid (NA) as part of the NAD salvage pathway for recycling NAD. PNC-1(ku212) is predicted to be a truncated protein missing the last 8 amino acids. Although the function of Pnc1 has been extensively studied in longevity in yeast, little is known about its roles in development. C. elegans pnc-1 clearly participates in a variety of developmental processes as demonstrated by multiple developmental defects in the loss-of-function pnc-1(ku212) mutants. The impaired nicotinamidase activity could result in high levels of NAM or low levels of NAD, leading to the developmental defects in the mutants. Two isoforms of pnc-1 including pnc-1a (with a signal sequence) and pnc-1b (without a signal sequence) are present in C. elegans. Another nicotinamidase Y57G11C.47, or pnc-2, is identified in this study by its ability to rescue pnc-1(ku212) phenotypes. How pnc-1 functions in development and how these three nicotinamidases
Functions of Vti1a and Vti1b in the Development of the Mouse Nervous System: Evidence from Double Knockout Mice

In eukaryotic cells molecules need to be transported to their correct intracellular destination without compromising the structural integrity of cellular compartments in order to maintain homoeostasis and to allow appropriate signalling cascades in certain space and time. To accomplish this, transport vesicles bud from an intracellular donor organelle and then target, dock and fuse with an acceptor organelle. SNARE (Soluble NSF attachment protein receptor) proteins have been implicated as central in membrane trafficking events. SNAREs vti1a and vti1b share 30% similarity in their amino acid sequences and have a distinct but overlapping subcellular localization. Vti1a has been associated with endosomal fusion and recycling processes after endocytosis whereas vti1b is connected with late endosomal fusion and lysosomal degradation events. Mice deficient of both endosomal SNARE proteins, vti1a and vti1b, die during intrauterine life just before birth, whereas single knockouts and triallelic mice survive and reach normal age without difficulty. These KO mice have various changes in central (CNS) as well as peripheral nervous system (PNS). In CNS they show wide ventricles and lack several fibre tracts including anterior commisure, hippocampal commisure, mammilothalamic, spinotrigeminal, corticospinal and pyramidal tracts. Corpus callosum thickness is greatly impaired in middle and thalamocortical axons cannot cross pallio-subpallial border. On the other hand only a few corticothalamic fibres can reach thalamus, overall data suggesting a deficit in membrane reorganization leading to impaired axon growth. Additionally, the KO mice also show alteration in cortical layering pattern. Layer 5 neurons are missing and layer 6 is expanded. This could be due to altered productivity in the ventricular zone during cortical layer development. The altered productivity may arise due to disturbances in cell polarity, failure in early decisions regarding lineage-specific differentiation from neural progenitors or any changes in signal ling molecules that could cause such consequences. On the other hand in PNS, KO mice show various degrees of neurodegeneration in different types of ganglia. Trigeminal (TG), dorsal root (DRG) and nodose-petrosal ganglia show severe neurodegeneration (up to 98%) whereas vestibular and cochlear ganglia show only 15-25% degeneration. This neurodegeneration may arise due to a lack of retrograde trafficking support during development of these ganglia or due to lack of delivering efficient plasma membrane required during axonal growth cone formation. Disparity in neurodegeneration among these ganglia could be due to the distance between the ganglia and their target. Unlike TG and DRG, vestibular and cochlear ganglia have less distant and therefore are able to survive. Overall phenotype suggests that vti1a and vti1b related endosomal functions are crucial for development of central as well as peripheral nervous system.
Nesting of the sooty Shearwater in Australia

The first recorded breeding of the Sooty Shearwater Puffinus griseus in Australia was reported by Rohu (1914). He collected a specimen and "eggs" on 29 December 1912 on Broughton Island, NSW. A check of the H.L. White Collection in the National Museum, Melbourne, revealed that a "clutch of one egg . " was collected. Since that first report a number of published records have appeared; all refer to islands off New South Wales and Tasmania.
UNSUPERVISED MULTI-CONSTRAINT DEEP NEURAL NETWORK FOR DENSE IMAGE MATCHING

Abstract. Dense image matching is essential to photogrammetry applications, including Digital Surface Model (DSM) generation, three dimensional (3D) reconstruction, and object detection and recognition. The development of an efficient and robust method for dense image matching has been one of the technical challenges due to high variations in illumination and ground features of aerial images of large areas. Nowadays, due to the development of deep learning technology, deep neural network-based algorithms outperform traditional methods on a variety of tasks such as object detection, semantic segmentation and stereo matching. The proposed network includes cost-volume computation, cost-volume aggregation, and disparity prediction. It starts with a pre-trained VGG-16 network as a backend and using the U-net architecture with nine layers for feature map extraction and a correlation layer for cost volume calculation, after that a guided filter based cost aggregation is adopted for cost volume filtering and finally the soft Argmax function is utilized for disparity prediction. The experimental conducted on a UAV dataset demonstrated that the proposed method achieved the RMSE (root mean square error) of the reprojection error better than 1 pixel in image coordinate and in-ground positioning accuracy within 2.5 ground sample distance. The comparison experiments on KITTI 2015 dataset shows the proposed unsupervised method even comparably with other supervised methods.
Beyond Tests

Automated program repair is an emerging technology that seeks to automatically rectify program errors and vulnerabilities. Repair techniques are driven by a correctness criterion that is often in the form of a test suite. Such test-based repair may produce overfitting patches, where the patches produced fail on tests outside the test suite driving the repair. In this work, we present a repair method that fixes program vulnerabilities without the need for a voluminous test suite. Given a vulnerability as evidenced by an exploit, the technique extracts a constraint representing the vulnerability with the help of sanitizers. The extracted constraint serves as a proof obligation that our synthesized patch should satisfy. The proof obligation is met by propagating the extracted constraint to locations that are deemed to be “suitable” fix locations. An implementation of our approach (ExtractFix) on top of the KLEE symbolic execution engine shows its efficacy in fixing a wide range of vulnerabilities taken from the ManyBugs benchmark, real-world CVEs and Google’s OSS-Fuzz framework. We believe that our work presents a way forward for the overfitting problem in program repair by generalizing observable hazards/vulnerabilities (as constraint) from a single failing test or exploit.
Promoting Adaptive Reuse in Ontario: A Planning Policy Tool for Making the Best of Manufacturing Decline

The exodus of manufacturing jobs from industrialized cities has increasingly altered the way municipalities plan and cope with buildings and areas that once served as industrial and economic centres. Now these often derelict and costly structures sit as an eyesore in many communities which experience symptoms of post-industrialism. The practice of adaptive reuse is a unique concept of city building, where demolition and traditional brownfield redevelopment have been common practice. Though an already established method, adaptive reuse is becoming increasingly popular due to a greater intensity to protect heritage, reuse materials and structures, and offer unique architectural spaces, there has been a demand to reuse former industrial buildings for other uses such as commercial and recreational spaces. To achieve this, there must be sufficient policy in place to incentivize and mitigate the increase cost and risk which are usually associated with this type of development. This article will focus specifically on Ontario, Canada, and the current Official Plans of all 51 of the province’s cities, and how they are addressing adaptive reuse in former industrial areas and unique ways in which they address this problem. A content analysis of the documents showed that there is a wide difference in reuse contextualization and suggested policy directives. However, Cities in Ontario have proposed that affordable housing, intensification, revitalization in the urban core, and creating spaces for creative and vibrant industries can be addressed by the promotion of reuse in the community. For those with strong industrial history, the applicability of reuse allows for communities to preserve their industrial heritage, while at the same time shift uses to the new economy.