Miracle-dz/UniFAR-FTUs huggingface dataset:
Effect of human activity on habitat selection in the endangered Barbary macaque

The exponential growth of human population and infrastructure is significantly reducing the amount of ecological resources available for wild animals. We analyzed the effect of human activity on Barbary macaques Macaca sylvanus, an endangered species restricted to the fragmented forests of Morocco and Algeria, using location data from five social groups inhabiting Ifrane National Park, Morocco. We used a resource selection function to explore the effects of anthropogenic disturbance on macaque habitat selection, using nine natural, social, and anthropogenic disturbance variables as predictors. Forest cover, home range overlap, herding route proximity, and road proximity were all significant predictors of habitat use. Macaques avoided areas used by local shepherds, to reduce the risk of attack by shepherds’ dogs, but approached roads to increase the chances of provisioning by tourists. However, herding route and road use varied seasonally in line with levels of human use, suggesting that macaques may be navigating their environment strategically (in space and time) to balance food acquisition and risk avoidance. The results of this study highlight the importance of assessing human impact on habitat selection in both space and time. Our data on seasonal variations in macaques’ use of roads can help prevent road injuries, a major source of mortality for provisioned macaques, by focusing management efforts by national park workers in time and space. Furthermore, understanding when and where macaques seek provisioning from tourists can help combat provisioning, which negatively impacts macaque health, behavior, and susceptibility to poaching.
Haptic assistance that restricts use of redundant solutions is detrimental to motor learning

Understanding the use of haptic assistance to facilitate motor learning is a critical issue, especially in the context of tasks requiring control of motor variability. However, the question of how haptic assistance should be designed in tasks with redundancy, where multiple solutions are available, is currently unknown. Here we examined the effect of haptic assistance that either allowed or restricted the use of redundant solutions on the learning of a bimanual steering task. 60 college-aged participants practiced steered a single cursor placed in between their hands along a smooth W-shaped track of a certain width as quickly as possible. Haptic assistance was either applied at the ‘task’ level using a force channel that only constrained the cursor to the track, allowing for the use of different hand trajectories, or (ii) the ‘individual effector’ level using a force channel that constrained each hand to a specific trajectory. In addition, we also examined the effect of ‘fading’ – i.e., decreasing assistance with practice to reduce dependence on haptic assistance. Results showed all groups improved with practice - however, groups with haptic assistance at the individual effector level performed worse than those at the task level. Moreover, fading of assistance did not offer learning benefits over constant assistance. Overall, the results suggest that haptic assistance is not effective for motor learning when it restricts the use of redundant solutions.
Metastatik Over Kanserlerini Değerlendirmede PET / BT

Pek cok over Ca’li hasta birinci basamak tedaviyi takiben 2 yil icerisinde rekurrens acisindan yuksek risk altindadir. Gunumuzde rekurren hastaligin tespitinde CA125 serum duzeyleri, bilgisayarli tomografi (BT), manyetik rezonans goruntuleme (MRI) ve ultrasonografi (USG) kullanilmaktadir. Ancak bu goruntuleme metotlari arasinda BT en etkili ve kullanisli olanidir. Ancak vakalarin onemli bir kisminda bu goruntuleme teknikleri kesin sonuc veremez. Bazi hallerde supheli pozitif yada belirsiz sonuclar vermekte bazen ise CA 125 seviyeleri yuksek oldugu halde sonuclar negatif gelmektedir. Over kanserinin erken rekurrensine ait periton metastazlarini cok kucuk boyutlarda oldugunda noninvaziv tani zorlasmaktadir. Bazi durumlarda kucuk capli hastalik CA 125 duzeyleri yuksek hastalarda anatomik goruntulerde saptanamamaktadir. Pozitron emisyon tomografisi (PET) bu tip hasta grubundaki rekurren hastaligi saptamada faydali olabilir. Buna karsin pozitif PET sonuclari cerrahi acidan lokalizasyonu belirlemekte yetersiz kalmaktadir. Bu bakimdan fonksiyonel ve anatomik goruntulemenin beraber kullanildigi PET-BT rekurren hastaligi saptamada yuksek sensitivite ve spesifiteye sahip kullanisli bir goruntuleme teknigidir
Cleavage-furrow formation without F-actin in Chlamydomonas

Significance Studies of eukaryotic cell division have focused on the actomyosin ring, whose filaments of F-actin and myosin-II are hypothesized to generate the contractile force for ingression of the cleavage furrow. However, myosin-II has a very limited taxonomic distribution, whereas division by furrowing is much more widespread. We used the green alga Chlamydomonas reinhardtii to investigate how a furrow can form without myosin-II and the potential roles of F-actin in this process. Although F-actin was associated with ingressing furrows, its complete removal only modestly delayed furrowing, suggesting that an actin-independent mechanism (possibly involving microtubules) drives furrow ingression. Such a mechanism presumably emerged early in eukaryotic evolution and may still underlie cell division in a diverse range of modern species. It is widely believed that cleavage-furrow formation during cytokinesis is driven by the contraction of a ring containing F-actin and type-II myosin. However, even in cells that have such rings, they are not always essential for furrow formation. Moreover, many taxonomically diverse eukaryotic cells divide by furrowing but have no type-II myosin, making it unlikely that an actomyosin ring drives furrowing. To explore this issue further, we have used one such organism, the green alga Chlamydomonas reinhardtii. We found that although F-actin is associated with the furrow region, none of the three myosins (of types VIII and XI) is localized there. Moreover, when F-actin was eliminated through a combination of a mutation and a drug, furrows still formed and the cells divided, although somewhat less efficiently than normal. Unexpectedly, division of the large Chlamydomonas chloroplast was delayed in the cells lacking F-actin; as this organelle lies directly in the path of the cleavage furrow, this delay may explain, at least in part, the delay in cytokinesis itself. Earlier studies had shown an association of microtubules with the cleavage furrow, and we used a fluorescently tagged EB1 protein to show that microtubules are still associated with the furrows in the absence of F-actin, consistent with the possibility that the microtubules are important for furrow formation. We suggest that the actomyosin ring evolved as one way to improve the efficiency of a core process for furrow formation that was already present in ancestral eukaryotes.
TRACE: transcription factor footprinting using DNase I hypersensitivity data and DNA sequence

Transcription is tightly regulated by cis-regulatory DNA elements where transcription factors can bind. Thus, identification of transcription factor binding sites is key to understanding gene expression and whole regulatory networks within a cell. The standard approaches for TFBSs prediction such as position weight matrices (PWMs) and chromatin immunoprecipitation followed by sequencing (ChIP-seq) are widely used but have their drawbacks such as high false positive rates and limited antibody availability, respectively. Several computational footprinting algorithms have been developed to detect TFBSs by investigating chromatin accessibility patterns, but also have their limitations. To improve on these methods, we have developed a footprinting method to predict Transcription factor footpRints in Active Chromatin Elements (TRACE). Trace incorporates DNase-seq data and PWMs within a multivariate Hidden Markov Model (HMM) to detect footprint-like regions with matching motifs. Trace is an unsupervised method that accurately annotates binding sites for specific TFs automatically with no requirement on pre-generated candidate binding sites or ChIP-seq training data. Compared to published footprinting algorithms, TRACE has the best overall performance with the distinct advantage of targeting multiple motifs in a single model.
Novel strain analysis informs about injury susceptibility of the corpus callosum to repeated impacts

Abstract Increasing evidence for the cumulative effects of head trauma on structural integrity of the brain has emphasized the need to understand the relationship between tissue mechanic properties and injury susceptibility. Here, diffusion tensor imaging, helmet accelerometers and amplified magnetic resonance imaging were combined to gather insight about the region-specific vulnerability of the corpus callosum to microstructural changes in white-matter integrity upon exposure to sub-concussive impacts. A total of 33 male Canadian football players (meanage = 20.3 ± 1.4 years) were assessed at three time points during a football season (baseline pre-season, mid-season and post-season). The athletes were split into a LOW (N = 16) and HIGH (N = 17) exposure group based on the frequency of sub-concussive impacts sustained on a per-session basis, measured using the helmet-mounted accelerometers. Longitudinal decreases in fractional anisotropy were observed in anterior and posterior regions of the corpus callosum (average cluster size = 40.0 ± 4.4 voxels; P < 0.05, corrected) for athletes from the HIGH exposure group. These results suggest that the white-matter tract may be vulnerable to repetitive sub-concussive collisions sustained over the course of a football season. Using these findings as a basis for further investigation, a novel exploratory analysis of strain derived from sub-voxel motion of brain tissues in response to cardiac impulses was developed using amplified magnetic resonance imaging. This approach revealed specific differences in strain (and thus possibly stiffness) along the white-matter tract (P < 0.0001) suggesting a possible signature relationship between changes in white-matter integrity and tissue mechanical properties. In light of these findings, additional information about the viscoelastic behaviour of white-matter tissues may be imperative in elucidating the mechanisms responsible for region-specific differences in injury susceptibility observed, for instance, through changes in microstructural integrity following exposure to sub-concussive head impacts.
NILAI GLUKOSA DARAH DAN TOTAL PROTEIN PLASMA PADA SAPI SIMPO YANG MENDERITA TREMATODIASIS DI PETERNAKAN RAKYAT DESA LABUHAN RATU KABUPATEN LAMPUNG TIMUR

The research aims to determine the value of blood glucose and plasma total protein in Simpo cattle suffering from trematodiasis . The research was conducted in December 2018 by taking blood samples of Simpo cattle in East Lampung. The research design used Completely Randomized Design (CRD) with 3 treatments and 4 replications from Simpo cow blood samples. The treatment used is P0: Simpo cattle which are not infested by worms; P1: Simpo cattle infested with 1 type of worm; and P2: Simpo cattle infested with 2 types of worms. Blood glucose value were analyzed in Biolab Indonesia Partner and total plasma were analyzed at Lampung Veterinary Center. Data from the observations were analyze using variance at the real level (P 0,10) on total plasma protein. The highest number of blood glucose values at P0(65,00 mg / dL) and the lowest at P1 (56,75 mg / dL). Total plasma protein at P0 (7,20 g / dL), P1 (7,30 g / dL), and P2 (6,95 g / dL). Key word : Blood glucose, Total plasma protein, Simpo cattle, Trematodiasis , Traditional farmer
PhyB induces intron retention and uORF-mediated translational inhibition of PIF3

The phytochrome B (phyB) photoreceptor stimulates light responses in plants in part by inactivating repressors of light responses such as phytochrome-interacting factor 3 (PIF3). It has been established that activated phyB inhibits PIF3 by rapid protein degradation and decreased transcription. PIF3 protein degradation has been shown to be mediated by EIN3-BINDING F-BOX PROTEIN (EBF) and LIGHT-RESPONSE BTB (LRB) E3 ligases, the latter simultaneously targeting phyB for degradation. In this study, we show that PIF3 level is additionally regulated by alternative splicing and protein translation. Overaccumulation of photo-activated phyB, which occur in the mutant defective for LRB genes under continuous red light (Rc), induces a specific alternative splicing of PIF3 that results in retention of an intron in the 5’UTR of PIF3 mRNA. In turn, the upstream opening reading frames (uORF) contained within this intron inhibit PIF3 protein synthesis. The phyB-dependent alternative splicing of PIF3 is diurnally regulated under the short-day light cycle. We hypothesize that this reversible regulatory mechanism may be utilized to fine-tune the level of PIF3 protein in light-grown plants, and may contribute to the oscillation of PIF3 protein abundance under the short-day environment. One Sentence Summary Light down-regulates PIF3 by multiple mechanisms. We show that phyB induces an alternative splicing event that inhibits PIF3 protein translation, and that is regulated by short-day diurnal cycle.
Anaphylaxis and anaesthesia - can treating a cough kill?

In Australia, anaphylaxis during surgery has been estimated to occur in approximately 1 in 10 000 cases. The mortality rate is approximately 4%, with long-term brain injury in an additional 2% of cases. Neuromuscular blocking drugs are responsible for approximately 60% of intraoperative anaphylaxis. Anaphylaxis is twice as likely to occur during surgery when a muscle relaxant is used.
Phase I study of MK-3475 (anti-PD-1 monoclonal antibody) in patients with advanced solid tumors.

2512 Background: Programmed death-1 (PD-1) is an inhibitory T-cell coreceptor that may lead to suppression of antitumor immunity. MK-3475 is a humanized monoclonal IgG4 antibody against PD-1. Preclinically, MK-3475 has shown antitumor activity in multiple tumor types. This first-in-human phase I trial explored safety, PK, PD, and antitumor activity of MK-3475. Methods: An open-label, dose escalation study was conducted in patients with advanced malignancy refractory to standard therapy. Cohorts of 3-6 patients were enrolled (3+3 design) at escalating IV doses of 1, 3, and 10 mg/kg. Following an initial dose and 28-day Cycle 1, patients were allowed to subsequently receive multiple doses given every 2 wks. Radiographic assessment was conducted every 8 wks using RECIST 1.1 guidelines. Results: Nine patients, 3 at each dose level, completed the dose-limiting toxicity (DLT) period (28 d). Patients had non–small cell lung cancer (NSCLC, n=3), rectal cancer (n=2), melanoma (MEL, n=2), sarcoma (n=1), or carcinoi.
Genetic engineering of Hoxb8-immortalized hematopoietic progenitors – a potent tool to study macrophage tissue migration

ABSTRACT Tumor-associated macrophages (TAMs) are detrimental in most cancers. Controlling their recruitment is thus potentially therapeutic. We previously found that TAMs perform protease-dependent mesenchymal migration in cancer, while macrophages perform amoeboid migration in other tissues. Inhibition of mesenchymal migration correlates with decreased TAM infiltration and tumor growth, providing rationale for a new cancer immunotherapy specifically targeting TAM motility. To identify new effectors of mesenchymal migration, we produced ER-Hoxb8-immortalized hematopoietic progenitors (cells with estrogen receptor-regulated Hoxb8 expression), which show unlimited proliferative ability in the presence of estrogen. The functionality of macrophages differentiated from ER-Hoxb8 progenitors was compared to bone marrow-derived macrophages (BMDMs). They polarized into M1- and M2-orientated macrophages, generated reactive oxygen species (ROS), ingested particles, formed podosomes, degraded the extracellular matrix, adopted amoeboid and mesenchymal migration in 3D, and infiltrated tumor explants ex vivo using mesenchymal migration. We also used the CRISPR/Cas9 system to disrupt gene expression of a known effector of mesenchymal migration, WASP (also known as WAS), to provide a proof of concept. We observed impaired podosome formation and mesenchymal migration capacity, thus recapitulating the phenotype of BMDM isolated from Wasp-knockout mice. Thus, we validate the use of ER-Hoxb8-immortalized macrophages as a potent tool to investigate macrophage functionalities. Summary: Validation of the use of ER-Hoxb8-immortalized hematopoietic progenitors combined with CRISPR/Cas9 technology as a potent tool to investigate macrophage functionalities with a large number of applications.
Monitoring of Plasmodium falciparum and Plasmodium vivax using microsatellite markers indicates limited changes in population structure after substantial transmission decline in Papua New Guinea

Monitoring the genetic structure of malaria parasite populations has been proposed as a novel and sensitive approach to quantify the impact of malaria control and elimination efforts. Here we describe the first population genetic analysis of sympatric Plasmodium falciparum (Pf) and Plasmodium vivax (Pv) populations following nationwide distribution of long-lasting insecticide treated nets (LLIN) in Papua New Guinea (PNG). Parasite isolates from serial cross-sectional studies pre-(2005-6) and post-LLIN (2010-2014) were genotyped using microsatellite markers. Despite parasite prevalence declining substantially in these communities (East Sepik: Pf=54.9-8.5%, Pv=35.7-5.6%, Madang: Pf=38.0-9.0%, Pv: 31.8-19.7%), genetically diverse and intermixing parasite populations remained. P. falciparum diversity declined modestly post-LLIN relative to pre-LLIN (East Sepik: Rs = 7.1-6.4, He = 0.77-0.71; Madang: Rs= 8.2-6.1, He = 0.79-0.71). Unexpectedly, population structure present in pre-LLIN populations was lost post-LLIN, suggesting that more frequent human movement between provinces may have contributed to higher gene flow between provinces. P. vivax prevalence initially declined but increased again in one province, yet diversity remained high throughout the study period (East Sepik: Rs=11.4-9.3, He=0.83-0.80; Madang: Rs=12.2-14.5, He=0.85-0.88). Although genetic differentiation values increased between provinces over time, no significant population structure was observed at any time point. For both species, the emergence of clonal transmission and significant multilocus linkage disequilibrium (mLD) due to increased focal inbreeding post-LLIN was a strong indicator of impact on the parasite population using these markers. After eight years of intensive malaria control in PNG and substantial prevalence decline the impact on parasite population diversity and structure detectable by microsatellite genotyping was limited.
Synthesis of low immunogenicity RNA with high-temperature in vitro transcription

The use of synthetic RNA for therapeutics requires that the in vitro synthesis process be robust and efficient. The technology used for the synthesis of these in vitro-transcribed mRNAs, predominantly using phage RNA polymerases (RNAPs), is well established. However, transcripts synthesized with RNAPs are known to display an immune-stimulatory activity in vivo, that is often undesirable. Previous studies have identified double-stranded RNA (dsRNA), a major by-product of the in vitro transcription (IVT) process, as a trigger of cellular immune responses. Here we describe the characterization of a high-temperature IVT process using thermostable T7 RNAPs to synthesize functional mRNAs that demonstrate reduced immunogenicity without the need for a post-synthesis purification step. We identify features that drive the production of two kinds of dsRNA by-products—one arising from 3’ extension of the run-off product and one formed by the production of antisense RNAs—and demonstrate that at a high temperature, T7 RNAP has reduced 3’-self extension of the run-off product. We show that template-encoded poly-A tailing does not affect 3’-self extension but reduces the formation of the antisense RNA by-products and that combining high-temperature IVT with template-encoded poly-A tailing prevents formation of both kinds of by-products.
The Role of Background Bacteria in Preventing the Isolation and Detection of Shigella and STEC in Foods and Novel MuSIC ddPCR Method to Improve STEC Detection in the Presence of Background Bacteria

Foodborne illness caused by Enterohemorrhagic E. coli (EHEC) and Shigella remain a public health issue in developed countries. The current microbiological methods for detecting EHEC and Shigella typically involve an enrichment step that aims to amplify the pathogenic organisms relative to the background bacteria flora present in foods. Following enrichment, there is a screening step to identify pathogens based on presence of virulence genes (ex. stx and eae for EHEC). False-positive detection of EHEC can occur if virulence targets are present within the population of bacteria found in foods, but not in any single organism. In this study, a Multiplexed Single Intact Cell ddPCR (MuSIC ddPCR) was developed to reduce the false-positives in the EHEC method. During enrichment, EHEC and Shigella are often outcompeted by non-target bacteria. The role of microbial antagonism of non-target bacteria in preventing growth of EHEC and Shigella in enrichment culture was also investigated.
Adaptasi dan Keragaan Hasil Varietas Unggul Padi di Lahan Rawa Wilayah Perbatasan Kalimantan Barat

Farmers cultivated rice once a year during the rainy season uses Cilosari variety with low yield (2.35 t/ha) in Matang Danau Village, Paloh Sub District, Sambas District, West Kalimantan Province. Increasing cropping index could be done by water pumping in dry season planting and using high yield adaptable varieties. The purpose of this research was to evaluate the adaptability and performance yield of highly rice variety in swamp lands West Kalimantan Border Area. The field experiment was carried out in Matang Danau village, Paloh Sub District, Sambas District, West Kalimantan Province, in the dry season from Maret to July 2018 and in the wet season from Oktober 2018 to February 2019. The research was arranged in randomized completely block design, with 3 replicates. The varieties tested, i.e., Inpara 1, 2, 3, 4, 6, 8, 9, Inpari 32, and check varieties Margasari and Cilosari. The results of the varieties adaptation test showed that there were differences in adaptation of varieties tested in swamps. Based on the results of the Inpara 1 variety, the highest yield was 6.6 t/ha, while the other varieties produced between 3.98-5.90 t/ha. The highest increasing yield compared to the varieties Margasari and Cilosari, i.e. Inpara 1. The increasing yield of rice in rainy season planting was higher 89,4% than that of the dry season.