Miracle-dz/UniFAR-FTUs huggingface dataset:
Interesting Paths in the Mapper

The Mapper produces a compact summary of high dimensional data as a simplicial complex. We study the problem of quantifying the interestingness of subpopulations in a Mapper, which appear as long paths, flares, or loops. First, we create a weighted directed graph G using the 1-skeleton of the Mapper. We use the average values at the vertices of a target function to direct edges (from low to high). The difference between the average values at vertices (high-low) is set as its weight. Covariation of the remaining h functions (independent variables) is captured by a h-bit binary signature assigned to the edge. An interesting path in G is a directed path whose edges all have the same signature. We define the interestingness score of such a path as a sum of its edge weights multiplied by a nonlinear function of their ranks in the path. Second, we study three optimization problems on this graph G. In the problem Max-IP, we seek an interesting path in G with the maximum interestingness score. We show that Max-IP is NP-complete. For the special case when G is a directed acyclic graph (DAG), we show that Max-IP can be solved in polynomial time - in O(mnd_i) where d_i is the maximum indegree of a vertex in G. In the more general problem IP, the goal is to find a collection of interesting paths such that these paths form an exact cover of E (hence they are edge-disjoint) and the overall sum of interestingness scores of all paths is maximized. We also study a variant of IP termed k-IP, where the goal is to identify a collection of edge-disjoint interesting paths each with k edges, and the total interestingness score of all paths is maximized. While k-IP can be solved in polynomial time for k = 3. Further, we show that k-IP remains NP-complete for k >= 3 even for the case when G is a DAG. We develop polynomial time heuristics for IP and k-IP on DAGs.
System design to prevent Ventilator Associated Pneumonia

Ventilator Associated Pneumonia (VAP) is a major problem in hospitals and is the leading cause of deaths among all hospital-acquired infections. Critically ill subjects who are in the intensive care unit (ICU) and under mechanical ventilator support are more prone to VAP. Traditionally, VAP bundle is used in hospitals for prevention of VAP. VAP bundle consists of five protocols which must be observed by the caregiver at regular intervals of time. One of the critical protocol steps is to always maintain the patient's head up angle at 30–45 degrees. This is not always strictly followed by caregivers due to lack of continuous monitoring and alert mechanisms. Hence a novel method is proposed which includes a wearable sensor which is attached to the patient's body, continuously monitoring the patient's head up angle and a tablet-based system that reminds the caregiver as and when required to help comply with the VAP bundle protocols. Preliminary studies under a controlled setting revealed that the system can continuously monitor and accurately detect the patient's head up angle and remind the caregiver when required.
Synthetic MicroProteins: Versatile Tools for Posttranslational Regulation of Target Proteins1[OPEN]

A synthetic microProtein approach unravels modes of posttranslational regulation of a wide range of protein families in Arabidopsis. MicroProteins are small, single-domain proteins that regulate multidomain proteins by sequestering them into novel, often nonproductive, complexes. Several microProteins have been identified in plants and animals, most of which negatively regulate transcription factors. MicroProtein candidates that potentially target a wide range of different protein classes were recently identified in a computational approach. Here, we classified all Arabidopsis (Arabidopsis thaliana) microProteins and developed a synthetic microProtein approach to target specific protein classes, such as hydrolases, receptors, and lyases, in a proof-of-concept approach. Our findings reveal that microProteins can be used to influence different physiological processes, which makes them useful tools for posttranslational regulation in plants and potentially also in animals.
Improvement of formability of high strength steel sheets in shrink flanging

In the shrinkage flanging, the wrinkling tends to occur due to compressive stress. The wrinkling will cause a difficulty in assembling parts, and severe wrinkling may leads to rupture of parts. The shrinkage flange of the ultra-high strength steel sheets not only defects the product by the occurrence of the wrinkling but also causes seizure and wear of the dies and shortens the life of dies. In the present study, a shape of a punch having gradual contact was optimized in order to prevent the wrinkling in shrinkage flanging of ultra-high strength steel sheets. The sheet was gradually bent from the corner of the sheet to reduce the compressive stress. The wrinkling in the shrink flanging of the ultra-high strength steel sheets was prevented by the punch having gradual contact. It was found that the punch having gradual contact is effective in preventing the occurrence of wrinkling in the shrinkage flanging.
Pregnancy Experiences of Female Sex Workers in Adama City, Ethiopia: Complexity of Partner Relationships and Pregnancy Intentions

Research and programs for female sex workers (FSWs) tend to focus exclusively on HIV prevention, with little attention paid to how pregnancy affects their lives. We examine the circumstances surrounding pregnancy and childbirth among women selling sex in Ethiopia. In Adama City, researchers asked 30 FSWs aged 18 and older who had ever been pregnant to participate in in‐depth interviews. The women reported on pregnancies experienced both before and after they had begun selling sex. They identified some of the fathers as clients, former partners, and current partners, but they did not know the identities of the other fathers. Missed injections, skipped pills, and inconsistent condom use were causes of unintended pregnancy. Abortion was common, typically with a medication regimen at a facility. Comprehensive sexual and reproductive health services should be provided to women who sell sex, in recognition and support of their need for family planning and their desire to plan whether and when to have children.
Vida y productividad de la herramienta de corte en el fresado de acabado del acero endurecido AISI D6

espanolEl fresado de acabado de aceros endurecidos con altas velocidades ha sido limitado por el desgaste prematuro de la herramienta y la inestabilidad dinamica. Durante el fresado de acabado de superficies inclinadas con fresas de espiga de punta redonda, ocurren elevadas interrupciones durante el corte y aparecen fenomenos dinamicos diferentes a aquellos que se presentan durante el fresado de superficies planas. En este trabajo se investiga la influencia de la estabilidad dinamica en la eficiencia y la productividad del fresado de acabado de superficies inclinadas de acero herramental endurecido AISI D6 con altas velocidades. Los experimentos fueron realizados en un centro de mecanizado MORI SEIKI SV40 con mando CNC. En los ensayos se emplearon herramientas intercambiables de carburos cementados y dos portaherramientas, una de acero y otro de carburo cementado. La evaluacion de la estabilidad dinamica se baso en el analisis de los espectros de frecuencias de las fuerzas de corte radial obtenidos mediante la Transformada Rapida de Fourier (FFT) y de la Raiz Media Cuadratica (RMS) de las senales de fuerza en el dominio del tiempo. Se comprobo que en los procesos mas estables, el volumen de viruta removido y el area cortada por la herramienta son mayores, produciendose un aumento de la productividad del proceso y obteniendose ademas un aumento de la vida util de la herramienta y mejores resultados en el acabado superficial de la pieza. EnglishFinish milling of hardened steels at high speed has been limited by premature tool wear and dynamic instability. During finish milling of inclined surfaces with ball end mill, high interruptions occur during cutting and dynamic phenomena different to those that occur during milling flat surfaces. In this work the influence of dynamic stability in efficiency and productivity of inclined surface finish milling in hardened steel AISI D6 with high speeds, was studied. The experiments were performed on a machining center MORI SEIKI SV40 with CNC control. They were used as well, interchangeable carbide tools and two tool holder, one of steel and the other of carbide. The evaluation of the dynamic stability was based on the analysis of the spectra frequency of cutting radial forces obtained through Fast Fourier Transform (FFT) and Root Main Square (RMS) of the signal in time domain. It was confirmed that in more stable processes, the volume of removed chip and the cut area by the tool are larger, resulting in an increase of the process productivity and obtaining besides an increase of the tool life and better results in the surface finish workpiece.
Association of Plasma Neurofilament Light Chain with Neocortical Amyloid-β Load and Cognitive Performance in Cognitively Normal Elderly Participants.

BACKGROUND The disruption of neurofilament, an axonal cytoskeletal protein, in neurodegenerative conditions may result in neuronal damage and its release into the cerebrospinal fluid and blood. In Alzheimer's disease (AD), neurofilament light chain (NFL), a neurofilament subunit, is elevated in the cerebrospinal fluid and blood. OBJECTIVE Investigate the association of plasma NFL with preclinical-AD features, such as high neocortical amyloid-β load (NAL) and subjective memory complaints, and cognitive performance in cognitively normal older adults. METHODS Plasma NFL concentrations were measured employing the single molecule array platform in participants from the Kerr Anglican Retirement Village Initiative in Ageing Health cohort, aged 65- 90 years. Participants underwent a battery of neuropsychological testing to evaluate cognitive performance and were categorized as low NAL (NAL-, n = 65) and high NAL (NAL+, n = 35) assessed via PET, and further stratified into subjective memory complainers (SMC; nNAL- = 51, nNAL+ = 25) and non-SMC (nNAL- = 14, nNAL+ = 10) based on the Memory Assessment Clinic- Questionnaire. RESULTS Plasma NFL inversely correlated with cognitive performance. No significant difference in NFL was observed between NAL+ and NAL- participants; however, within APOEɛ4 non-carriers, higher NAL was observed in individuals with NFL concentrations within quartiles 3 and 4 (versus quartile 1). Additionally, within the NAL+ participants, SMC had a trend of higher NFL compared to non-SMC. CONCLUSION Plasma NFL is inversely associated with cognitive performance in elderly individuals. While plasma NFL may not reflect NAL in individuals with normal global cognition, the current observations indicate that onset of axonal injury, reflected by increased plasma NFL, within the preclinical phase of AD may contribute to the pathogenesis of AD.
Production of 2-Hydroxyisobutyric Acid from Methanol by Methylobacterium extorquens AM1 Expressing (R)-3-Hydroxybutyryl Coenzyme A-Isomerizing Enzymes

ABSTRACT The biotechnological production of the methyl methacrylate precursor 2-hydroxyisobutyric acid (2-HIBA) via bacterial poly-3-hydroxybutyrate (PHB) overflow metabolism requires suitable (R)-3-hydroxybutyryl coenzyme A (CoA)-specific coenzyme B12-dependent mutases (RCM). Here, we characterized a predicted mutase from Bacillus massiliosenegalensis JC6 as a mesophilic RCM closely related to the thermophilic enzyme previously identified in Kyrpidia tusciae DSM 2912 (M.-T. Weichler et al., Appl Environ Microbiol 81:4564–4572, 2015, https://doi.org/10.1128/AEM.00716-15 ). Using both RCM variants, 2-HIBA production from methanol was studied in fed-batch bioreactor experiments with recombinant Methylobacterium extorquens AM1. After complete nitrogen consumption, the concomitant formation of PHB and 2-HIBA was achieved, indicating that both sets of RCM genes were successfully expressed. However, although identical vector systems and incubation conditions were chosen, the metabolic activity of the variant bearing the RCM genes from strain DSM 2912 was severely inhibited, likely due to the negative effects caused by heterologous expression. In contrast, the biomass yield of the variant expressing the JC6 genes was close to the wild-type performance, and 2-HIBA titers of 2.1 g liter−1 could be demonstrated. In this case, up to 24% of the substrate channeled into overflow metabolism was converted to the mutase product, and maximal combined 2-HIBA plus PHB yields from methanol of 0.11 g g−1 were achieved. Reverse transcription-quantitative PCR analysis revealed that metabolic genes, such as methanol dehydrogenase and acetoacetyl-CoA reductase genes, are strongly downregulated after exponential growth, which currently prevents a prolonged overflow phase, thus preventing higher product yields with strain AM1. IMPORTANCE In this study, we genetically modified a methylotrophic bacterium in order to channel intermediates of its overflow metabolism to the C4 carboxylic acid 2-hydroxyisobutyric acid, a precursor of acrylic glass. This has implications for biotechnology, as it shows that reduced C1 substrates, such as methanol and formic acid, can be alternative feedstocks for producing today's commodities. We found that product titers and yields depend more on host physiology than on the activity of the introduced heterologous function modifying the overflow metabolism. In addition, we show that the fitness of recombinant strains substantially varies when they express orthologous genes from different origins. Further studies are needed to extend the overflow production phase in methylotrophic microorganisms for the implementation of biotechnological processes.
Effective biomedical document classification for identifying publications relevant to the mouse Gene Expression Database (GXD)

Abstract The Gene Expression Database (GXD) is a comprehensive online database within the Mouse Genome Informatics resource, aiming to provide available information about endogenous gene expression during mouse development. The information stems primarily from many thousands of biomedical publications that database curators must go through and read. Given the very large number of biomedical papers published each year, automatic document classification plays an important role in biomedical research. Specifically, an effective and efficient document classifier is needed for supporting the GXD annotation workflow. We present here an effective yet relatively simple classification scheme, which uses readily available tools while employing feature selection, aiming to assist curators in identifying publications relevant to GXD. We examine the performance of our method over a large manually curated dataset, consisting of more than 25 000 PubMed abstracts, of which about half are curated as relevant to GXD while the other half as irrelevant to GXD. In addition to text from title-and-abstract, we also consider image captions, an important information source that we integrate into our method. We apply a captions-based classifier to a subset of about 3300 documents, for which the full text of the curated articles is available. The results demonstrate that our proposed approach is robust and effectively addresses the GXD document classification. Moreover, using information obtained from image captions clearly improves performance, compared to title and abstract alone, affirming the utility of image captions as a substantial evidence source for automatically determining the relevance of biomedical publications to a specific subject area. Database URL: www.informatics. jax.org
Improved survival using intensity‐modulated radiation therapy in head and neck cancers: A SEER‐Medicare analysis

Intensity‐modulated radiation therapy (IMRT) is a technologically advanced, and more expensive, method of delivering radiation therapy with a goal of minimizing toxicity. It has been widely adopted for head and neck cancers; however, its comparative impact on cancer control and survival remains unknown. The goal of this analysis was to compare the cause‐specific survival (CSS) for patients with head and neck cancers treated with IMRT versus non‐IMRT from 1999 to 2007.
An update on equine post‐operative ileus: Definitions, pathophysiology and management

Post-operative ileus (POI) is a serious condition which any horse undergoing abdominal surgery is at risk of developing, leading to increased hospitalisation time and resulting costs. Advances in the understanding of the development of equine POI are mainly based on human and rodent literature, where manipulation-induced inflammation has been identified as a trigger, with activation of resident muscularis externa macrophages playing a crucial role in the pathophysiology. Despite many pharmacological trials in all species, there is no single completely successful treatment for POI, highlighting that the condition is multifactorial in cause and requires a multimodal approach to minimise its incidence.
Time-Course Transcriptomics Analysis Reveals Key Responses of Submerged Deepwater Rice to Flooding1

Comparative transcriptomics and targeted analyses provide insights into the roles of phytohormone synthesis, signaling, and turnover during submergence-induced internode elongation in deepwater rice. Water submergence is an environmental factor that limits plant growth and survival. Deepwater rice (Oryza sativa) adapts to submergence by rapidly elongating its internodes and thereby maintaining its leaves above the water surface. We performed a comparative RNA sequencing transcriptome analysis of the shoot base region, including basal nodes, internodes, and shoot apices of seedlings at two developmental stages from two varieties with contrasting deepwater growth responses. A transcriptomic comparison between deepwater rice cv C9285 and nondeepwater rice cv Taichung 65 revealed both similar and differential expression patterns between the two genotypes during submergence. The expression of genes related to gibberellin biosynthesis, trehalose biosynthesis, anaerobic fermentation, cell wall modification, and transcription factors that include ethylene-responsive factors was significantly different between the varieties. Interestingly, in both varieties, the jasmonic acid content at the shoot base decreased during submergence, while exogenous jasmonic acid inhibited submergence-induced internode elongation in cv C9285, suggesting that jasmonic acid plays a role in the submergence response of rice. Furthermore, a targeted de novo transcript assembly revealed transcripts that were specific to cv C9285, including submergence-induced biotic stress-related genes. Our multifaceted transcriptome approach using the rice shoot base region illustrates a differential response to submergence between deepwater and nondeepwater rice. Jasmonic acid metabolism appears to participate in the submergence-mediated internode elongation response of deepwater rice.
Pseudo-Static Experiment on Abnormal SRC Joints with Beams at Different Level

The steel reinforced concrete abnormal joints of the coal-fired power plant frame-bent structures were studied through pseudo-static experiment for the technological requirements.The SRC abnormal joints failure modes,the joints strength degradation,skeleton curve and hysteretic curve were obtained.The facters to influence the performance of profiled steel reinforced concrete joints,including the differential height of beams,loading direction were discussed.It was found that with the increase of differential height,the abnormal joint fails like a side joint,the central of abnormal joint looks like a short column and the abnormal joint strength increases.The abnormal joints strength under positive loading is higher than that under negative load,as the differential height increases,the asymmetric behavior of hysteresis curves can be seen obviously.The abnormal joints with steel reinforced concrete beams have better seismic performance.
Genome-wide DNA Methylation Profiling Reveals Methylation Markers Associated with 3q Gain for Detection of Cervical Precancer and Cancer

Purpose: Epigenetic host cell changes involved in cervical cancer development following a persistent high-risk human papillomavirus (hrHPV) infection, provide promising markers for the management of hrHPV-positive women. In particular, markers based on DNA methylation of tumor suppressor gene promoters are valuable. These markers ideally identify hrHPV-positive women with precancer (CIN2/3) in need of treatment. Here, we set out to identify biologically relevant methylation markers by genome-wide methylation analysis of both hrHPV-transformed cell lines and cervical tissue specimens. Experimental Design and Results: Genome-wide discovery by next-generation sequencing (NGS) of methyl-binding domain–enriched DNA (MBD-Seq) yielded 20 candidate methylation target genes. Further verification and validation by multiplex-targeted bisulfite NGS and (quantitative) methylation-specific PCR (MSP) resulted in 3 genes (GHSR, SST, and ZIC1) that showed a significant increase in methylation with severity of disease in both tissue specimens and cervical scrapes (P < 0.005). The area under the ROC curve for CIN3 or worse varied between 0.86 and 0.89. Within the group of CIN2/3, methylation levels of all 3 genes increased with duration of lesion existence (P < 0.0005), characterized by duration of preceding hrHPV infection, and were significantly higher in the presence of a 3q gain (P < 0.05) in the corresponding tissue biopsy. Conclusions: By unbiased genome-wide DNA methylation profiling and comprehensive stepwise verification and validation studies using in vitro and patient-derived samples, we identified 3 promising methylation markers (GHSR, SST, and ZIC1) associated with a 3q gain for the detection of cervical (pre)cancer. Clin Cancer Res; 23(14); 3813–22. ©2017 AACR.