SIRIS-Lab/unlabelled-sti-corpus huggingface dataset:
Shaping the landscape of the<i>Escherichia coli</i>chromosome: replication-transcription encounters in cells with an ectopic replication origin

Each cell division requires the unwinding of millions of DNA base pairs to allow chromosome duplication and gene transcription. As DNA replication and transcription share the same template, conflicts between both processes are unavoidable and head-on collisions are thought to be particularly problematic. Surprisingly, a recent study reported unperturbed cell cycle progression in Escherichia coli cells with an ectopic replication origin in which highly transcribed rrn operons were forced to be replicated opposite to normal. In this study we have re-generated a similar strain and found the doubling time to be twice that of normal cells. Replication profiles of this background revealed significant deviations in comparison to wild-type profiles, particularly in highly transcribed regions and the termination area. These deviations were alleviated by mutations that either inactivate the termination area or destabilise RNA polymerase complexes and allow their easier displacement by replication forks. Our data demonstrate that head-on replication-transcription conflicts are highly problematic. Indeed, analysis of the replication profile of the previously published E. coli construct revealed a chromosomal rearrangement that alleviates replication-transcription conflicts in an intriguingly simple way. Our data support the idea that avoiding head-on collisions has significantly contributed to shaping the distinct architecture of bacterial chromosomes.
Comparative antioxidant responses in liver of Carassius auratus exposed to phthalates: An integrated biomarker approach

Phthalates (PAEs) are chemical agents typically used as plasticizers in numerous industrial products. They have become ubiquitous contaminants due to their tendency to release into the environment. The present study was conducted to investigate the comparative antioxidant responses in liver of freshwater goldfish Carassius auratus injected intraperitoneally with 17 different PAEs at a concentration of 10 mg/kg for 10 days. The results indicated that these PAEs can adversely affect the antioxidant status, confirmed by the significantly inhibited activities of antioxidant enzymes (superoxide dismutase, catalase, and glutathione peroxidase). Especially, the latter two enzymes constituted the most affected antioxidant enzymes after the exposure, and the lowest values were recorded for the catalase activity. The toxicity order was proposed via the integrated biomarker response, with dicyclohexyl phthalate the most toxic and diethyl phthalate the least. Overall, these findings may contribute to the risk assessments of these chemicals on aquatic species.
The complete genome sequence of a novel mycovirus from Alternaria longipes strain HN28

The complete nucleotide sequence of Alternaria longipes dsRNA virus 1 (AlRV1), a novel double-stranded RNA (dsRNA) mycovirus, was determined and analyzed. AlRV1-HN28 contains a single dsRNA genome segment 3415 base pairs in length (excluding the 3' poly(A) tail) and was predicted to contain two discontiguous open reading frames (ORFs, ORF A and ORF B). The 5'-proximal ORF A (1182 nt) potentially encodes a protein of 394 amino acids (aa) with a predicted molecular mass of 43 kDa; this protein showed no significant similarities to any other sequences in any of the NCBI protein databases. The 3'-proximal ORF B (1737 nt) encodes a protein of 579 aa with a predicted molecular mass of 65 kDa; this protein sequence shares similarities with the conserved domains of RNA-dependent RNA polymerases of other mycoviruses. Phylogenetic analysis indicated that AlRV1-HN28 was closely related to four other unclassified viruses, which suggests that the AlRV1-HN28 isolated from Alternaria longipes may belong to a new family of dsRNA mycoviruses. This is the first report of the full-length nucleotide sequence of a mycovirus that infects Alternaria longipes.
The Alzheimer disease BIN1 locus as a modifier of GBA-associated Parkinson disease

GBA mutations are among the most common genetic risk factors for Parkinson disease (PD) worldwide. We aimed to identify genetic modifiers of the age at onset (AAO) in GBA-associated PD. The study included a genome-wide discovery phase, including a cohort of 79 patients with the GBA p.N370S mutation, and candidate validation and replication analyses of 8 SNPs in patients with mild (n = 113) and severe (n = 41) GBA mutations. Genotyping was performed using the Affymetrix human SNP 6.0 array and TaqMan assays. In the genome-wide phase, none of the SNPs passed the genome-wide significance threshold. Eight SNPs were selected for further analysis from the top hits. In all GBA-associated PD patients (n = 153), the BIN1 rs13403026 minor allele was associated with an older AAO (12.4 ± 5.9 years later, p = 0.0001), compared to patients homozygous for the major allele. Furthermore, the AAO was 10.7 ± 6.8 years later in patients with mild GBA mutations, (p = 0.005, validation group), and 17.1 ± 2.5 years later in patients with severe GBA mutations (p = 0.01, replication). Our results suggest that alterations in the BIN1 locus, previously associated with Alzheimer disease, may modify the AAO of GBA-associated PD. More studies in other populations are required to examine the role of BIN1-related variants in GBA-associated PD.
Uncovering the behavioural and neural correlates of joint action learning

The ability to perform joint (multi-person) actions such as ensemble music performance confers numerous benefits, from generating unique aesthetic experiences to enhancing affiliation with one’s co-actors. Co-actors must be able to accurately predict when one another’s actions will occur so that they can time their own actions accordingly. One question facing the field of social neuroscience is how co-actors learn to make accurate predictions about one another’s actions. The current project, JAL, launches one of the first systematic investigations of joint action learning to address this question on the levels of both brain and behaviour.  The project will implement a series of empirical studies in which partners learn novel joint turn-taking tasks while electroencephalography (EEG) is simultaneously measured from both partners: Turn-taking tasks are optimal for measuring prediction processes because partners must be able to accurately predict when one another’s turns will end so that they can seamlessly alternate actions.  Learning conditions will be manipulated across studies to address three primary questions: 1) Is there an identifiable neural marker of how well partners learn to predict one another’s actions? 2) Do partners learn to generate stronger predictions about actions that serve as relevant cues for interpersonal coordination relative to actions that do not? 3) Can partners acquire the ability to predict one another's actions in a task-general manner? Outcomes from these studies will provide novel insights into how humans learn to coordinate actions with one another and will pioneer methods of simultaneously measuring behavioural and neural activity from multiple individuals during action learning. The knowledge gained from this project will be critical not only for improving methods of teaching joint action but also for developing interventions for individuals with deficits in social motor coordination.
Dependable Risk-Aware Efficiency Improvement for Self-Organizing Emergent Systems

An efficiency improvement advisor agent acts as a consultation service for a self-organizing multi-agent system that improves operational efficiency. It identifies recurrent tasks in past problems that allow the creation of so-called exception rules for individual agents to limit future inefficient behavior. There exists the danger that introduced rules could possibly infringe on the flexibility and therefore reliability of the system. In this paper, we present a dependable risk-aware efficiency improvement advisor that uses Monte Carlo simulation techniques in strategic analysis assessing the long-term potential and risks of prospective rules. Our experimental evaluation, for the domain of dynamic pickup and delivery problems, shows that the result is a minimal, yet effective, set of risk-averse exception rules. These rules can be provided to individual agents to reliably achieve an overall long-term improvement in efficiency while maintaining flexibility.
Systems Approach to Knowledge Synthesis

This article presents a systems approach to knowledge synthesis or construction, starting with a new systems thinking named the informed systems thinking, which should serve as the basic tool of knowledge integration and support creativity. Based on this new systems thinking, a new systems approach to knowledge synthesis or construction has been developed as a systems methodology that consists of three fundamental parts: how to collect and synthesize knowledge, how to use our abilities in collecting knowledge, and how to justify the synthesized knowledge. This article first describes the informed systems thinking and then introduces a new systems approach to knowledge synthesis and the features of this new approach from a viewpoint of knowledge creation.
TARGETING OF FUEL OUTPUT BY OFF-AXIS DIRECTING OF NOZZLE OUTPUT STREAMS

Nozzles and method of making the same are disclosed. The disclosed nozzles have a non- coined three-dimensional inlet face and an outlet face opposite the inlet face. The nozzles may have one or more nozzle through-holes extending from the inlet face to the outlet face. Fuel injectors containing the nozzle are also disclosed. Methods of making and using nozzles and fuel injectors are further disclosed.
Characterization and use of microbial communities in Doenjang to control the unpleasant odor of Ginkgo epicarp

The Ginkgo epicarp is usually discarded due to contained butyric acid causing an unpleasant odor. Control of butyric acid in the Ginkgo epicarp was achieved by fermenting with doenjang under different fermentation conditions. The contents of butyric acid decreased 3.2× when Ginkgo epicarp was fermented at 30°C for 6 months. Microbes in doenjang were probably responsible for the reduction in the butyric acid content. Microbial communities were analyzed during fermentation. Communities were isolated using selective media and analyzed using metagenomic pyrosequencing based on 16S rRNA sequences. Changes in the microbial communities were confirmed at the species level. Staphylococcus gallinarum was the dominant species and maintained a constant level during fermentation. The possibility of a new fermented food with Ginkgo epicarp is suggested.
Photocloth: a framework to synthesize real-time photorealistic cloth animation from video input.

Computer Graphics is the area of computer science that studies methods for digitally synthesizing and animating visual content. Among all the potential contexts where computer graphics techniques can be used, cloth animation is a particularly interesting case since, in the real world, clothing is far more than just the physical objects that we wear; clothing is a key element to show someone’s expressiveness and motion, it even defines his or her identity. 

However, cloth animation is a complex and extremely high-dimensional problem. To digitally synthesize cloth animation, a large number of properties that affect the way cloth behaves need to be estimated: textures, deformations, collisions, materials, illumination, etc. 

Current approaches for cloth animation tried to overcome this challenging problem following two main trends: image-based methods use captured data to construct a low-dimensional model to digitally synthesize new animations, however they can only sample a small portion of the high-dimensional space of cloth and poses; the physics-based methods aim to simulate cloth only using mathematical equations that express physics laws, however, they are computationally expensive and have trouble replicating real-world behavior. 

This fellowship will investigate a new  model for cloth simulation that combines a physical-based method with image-based infomation to generate real-time believable cloth animation. The new model will use a multi-scale framework to handle the dynamic geometry and appearance at different levels of detail. The most salient dynamic geometric properties of the animation will be handled by a low-resolution representation of the cloth using a physics-based model, which reduces the high-dimensionality of the pose space to a lower-dimensional subspace.  Mid- and fine-scale details such as shading, wrinkles and appearance will be incorporated by an image-based approach, using the input imagery to learn to predict those properties.
Pengar som ristningar på träpinnar. Icke-monetära pengars funktion för fungerande lagbildningar

Notches on wooden sticks: the role of non-coin money in village organizationLocal money in the form of notched sticks played a significant role in selfregulated organization of exchange in villages in 16th- and 17th-century Sweden. This kind of money is an example of non-coin money that only existed as money of account, or more precisely only as notches on wooden sticks (tally-sticks).The article argues that it is impossible to speak of local money as an isolated unit. Instead, the money symbolized by notches was interwoven with credit-networks and social relations. This helps to explain how local money made cooperation possible. Moreover, the local money of account was connected to credit systems and social relations, which explains why adoption of modern credit forms as well as changes in social relations were slow to develop in many localities.Using a perspective based in accounting history and anthropology, which sees money as credit, this article contributes to heterodox theories of money that seeks to explain the functions and social relations of different kinds of money.The money system linked to the notched sticks can be seen as variation of today’s community currencies that make different social actions possible and which are constructed for special purposes. Often one stick was created for a specific activity. In other words, the farmers created their own money for different purposes. For example, there were turn-taking sticks for ploughing snow, feeding the bull, delivering the post or providing transportation for the local clergy etc. Such sticks were often connected to sticks that recorded failure to deliver services. Persons who had not done their daily work had to do more days of work in the future. Other sticks could be used to remember and calculate how much timber or workdays different farms contributed to buildings such as the common mill or saw and how much of it was used. Such sticks made it possible to calculate and ensure that rights and obligations were distributed according to egalitarian principles. In such cases money as notches was used as calculative money and made possible value reciprocity.The article is based on ethnographic and historical literature together with the Nordic Museum’s collection of notched sticks, including information about their usage; the Nordic museum’s questionnaires about village organization in the beginning of the 20th century; and private research archives.
LAMINATION FILM AND ADHESIVE THEREFOR

A film structure including: (a) at least one functionalized film layer, wherein the at least one film layer comprises a polar-reactive group polyolefin layer used as an internal layer in the film structure; and (b) a lamination adhesive composition present on, and in contact with, a least a portion of a surface of the internal layer; wherein the green tack value of the adhesive composition is greater than 0.772 Newtons/centimeter; a laminate including the above film structure bonded to a substrate layer; a process for producing the film structure; a process for producing the laminate; and a laminated article made from the above laminate.
EXCISABLE PLANT TRANSGENIC LOCI WITH SIGNATURE PROTOSPACER ADJACENT MOTIFS OR SIGNATURE GUIDE RNA RECOGNITION SITES

Transgenic plants comprising synthetic protospacer adjacent motifs (sPAMs) or synthetic guide RNA recognition sites introduced at or near the junctions the transgene insert with non-transgenic genomic DNA, methods of making such plants, and use of such plants to facilitate breeding are disclosed.
Survey of mycotic mastitis in dairy cows from Heilongjiang Province, China

A survey of the prevalence rate, pathogenic subspecies, and risk factors of mycotic mastitis in dairy cows from Heilongjiang Province, China, was conducted. Milk samples from 412 cows with chronic mastitis were collected and cultured on 8 % sheep blood agar, MacConkey agar, and Sabouraud agar with chloramphenicol. Counting of the morphologically distinct colonies was performed, as well as the isolation and identification of organisms through phenotypical and physiological criteria. Four hundred seventy-eight aerobic microorganisms were isolated. Yeasts and yeast-like fungi 35.6 % (170/478) and bacteria 64.4 % (308/478) were isolated. The fungal isolates were identified as Candida (79.4 %), Trichosporon (5.9 %), Aspergillus (7.1 %), Cryptococcus (2.4 %), and Rhodotorula (4.1 %). More than ten species of yeast were isolated including Candida krusei 50/135 (37 %), Candida rugosa 16/135 (11.9 %), and Candida lusitaniae 15/135 (11.1 %). A higher positivity (18.5 and 56.3 %) (P ≤0.05) was observed in cows from environmental temperatures of 0-15 and 15-35 °C than those at <0 °C and in cows affected by the disease for >45 and 30-45 days compared with cows suffering 10-30 days. Meanwhile, a statistically significant difference (44.9 vs. 31.4 %) (P ≤0.05) was observed under extensive raising systems vs. intensive raising systems. It appears that Candida is a major pathogen of mycotic mastitis of dairy cows. Extensive raising system, high environmental temperature (15-35 °C), and the duration of the disease (>30 days) were important risk factors of the incidence of mycotic mastitis. Here, we provide a theoretical foundation for research into preventing and treating mycotic mastitis of dairy cows in China.
Urinary collecting system invasion is associated with poor survival in patients with clear-cell renal cell carcinoma

To evaluate the prognostic significance of urinary collecting system invasion (UCSI) in a large series of patients with clear-cell renal cell carcinoma (RCC).Patients with clear-cell RCC treated with nephrectomy between 2001 and 2010 were reviewed from a prospectively maintained registry. One urological pathologist re-reviewed all slides. Cancer-specific survival was estimated using the Kaplan-Meier method, and associations of UCSI with death from RCC were evaluated using Cox models.Of the 859 patients with clear-cell RCC, 58 (6.8%) had UCSI. At last follow-up, 310 patients had died from RCC at a median of 1.8 years after surgery. The median follow-up for patients alive at last follow-up was 8.2 years. The estimated cancer-specific survival at 10 years after surgery for patients with UCSI was 17%, compared with 60% for patients without UCSI (P < 0.001). In a multivariable model, UCSI remained independently associated with an increased risk of death from RCC (hazard ratio 1.5; P = 0.018). Further, among patients with pT3 RCC, those with USCI had survival outcomes similar to those of patients with pT4 RCC.Collecting system invasion is associated with poor prognosis among patients with clear-cell RCC. If validated, consideration should be given to including UCSI in future staging systems.
Direct and indirect mechanisms of fisheries-induced evolution

Fisheries-induced evolution (FIE) represents one of the most important human-induced evolutionary pressures for natural populations. However, the exact mechanisms by which FIE operates is still unclear. Fish may vary in their vulnerability to capture (because of their life history and/or physiology or behaviour) and undergo heritable genetic change due to selection imposed by commercial fishing, resulting in a direct evolutionary response. Alternatively intense fishing could alter the population density of targeted fish causing an indirect environmental effect on the phenotypes (i.e. phenotypic plasticity) within the remaining fish population. This could also lead to density-dependent effects on the evolutionary responses, through genotype-by-environment interactions. A better understanding of the relative roles of direct and indirect sources of FIE could thus substantially increase the prospects of sustainable fisheries management. Using controlled experiments and simulated fisheries practices, the aims of this project are: (1) to document phenotypic (i.e. physiological, behavioural and life-history traits) and genetic differences in fish the most and least vulnerable to fishing within a generation (representing their initial responses to fishing and their evolutionary potential); (2) to determine how population density may alter the expression of traits related to vulnerability ; and (3) to investigate, in populations that have experienced selective fishing over generations, how vulnerability, population density and their interaction modulate phenotypic variation as source of FIE. This project will use innovative approaches to investigate the mechanisms underlying FIE such as experimentally assessing population density as environmental effect relevant to FIE, and directly merging molecular and quantitative genetics. This will provide completely novel insights into the broad importance of density effects on evolution, while addressing a key issue for FIE research.
A Rapid Automatic Processing Platform for Bead Label–Assisted Microarray Analysis

Molecular diagnostics using microarrays are increasingly being used in clinical diagnosis because of their high throughput, sensitivity, and accuracy. However, standard microarray processing takes several hours and involves manual steps during hybridization, slide clean up, and imaging. Here we describe the development of an integrated platform that automates these individual steps as well as significantly shortens the processing time and improves reproducibility. The platform integrates such key elements as a microfluidic chip, flow control system, temperature control system, imaging system, and automated analysis of clinical results. Bead labeling of microarray signals required a simple imaging system and allowed continuous monitoring of the microarray processing. To demonstrate utility, the automated platform was used to genotype hereditary hearing-loss gene mutations. Compared with conventional microarray processing procedures, the platform increases the efficiency and reproducibility of hybridization, speeding microarray processing through to result analysis. The platform also continuously monitors the microarray signals, which can be used to facilitate optimization of microarray processing conditions. In addition, the modular design of the platform lends itself to development of simultaneous processing of multiple microfluidic chips. We believe the novel features of the platform will benefit its use in clinical settings in which fast, low-complexity molecular genetic testing is required.