Miracle-dz/UniFAR-FTUs huggingface dataset:
Designing for Mixed-Initiative Interactions between Human and Autonomous Systems in Complex Environments

The purpose of the paper is to discuss human centered design implications for shared decision making between humans and autonomous systems in complex environments. Design implications are generated based on empirical results from two research paradigms. In the first paradigm, an intelligent agent (RoboLeader) supervised multiple subordinate systems and was in turn supervised by the human operator. The Robo Leader research varied number of subordinate units, task difficulty, agent reliability, type of agent errors, and partial autonomy. The second paradigm involved human interaction with partially and fully autonomous systems. Design implications from both paradigms are evaluated -- relating to multitasking, adaptive systems, false alarms, individual differences, operator trust, and allocation of human and agent tasks for partial autonomy. We conclude that mixed-initiative decision sharing depends on designing interfaces that support human-agent transparency.
Classification of handwritten documents : writer recognition

Malgre les predictions d'un monde sans papier et le developpement des documents electroniques, les documents manuscrits ont garde leur importance et les problemes de l'identification et de l'authentification des auteurs ont constitue un domaine de recherche actif au cours de ces dernieres annees. Nous avons developpe une methode efficace pour la reconnaissance automatique de scripteur a partir des images de texte manuscrit offline. Notre methode repose sur deux aspects differents de l'ecriture, la presence des formes redondantes dans l'ecriture et des attributs visuels de l'ecriture. En nous basant sur l'hypothese qu'un individu utilise certaines formes plus frequemment que les autres quand il ecrit, nous esperons extraire ces formes en analysant des petits fragments d'ecriture et en regroupant les formes similaires dans des classes. Ces classes sont determinees soit pour chacun des scripteurs separement ou pour un groupe de scripteurs generant un ensemble universel de formes. L'ecriture en question est ensuite comparee a ces classes de formes produites. Ensuite, nous exploitons les deux importants attributs visuels de l'ecriture, l'orientation et la courbure, qui permettent de distinguer une ecriture d'une autre. Ces attributs sont extraits par le calcul d'un ensemble de caracteristiques a differents niveaux d'observation. Deux ecritures sont ensuite comparees en calculant les distances entre leurs caracteristiques respectives. Enfin, nous combinons les deux facettes de l'ecriture pour caracteriser le scripteur d'un echantillon manuscrit. En utilisant ces caracteristiques, on obtient des taux d'identification qui sont comparables aux meilleurs resultats rapportes a ce jour pour l'identification de scripteur hors ligne.
TET‐catalyzed oxidation of intragenic 5‐methylcytosine regulates CTCF‐dependent alternative splicing

Intragenic 5‐methylcytosine and CTCF mediate opposing effects on pre‐mRNA splicing: CTCF promotes inclusion of weak upstream exons through RNA polymerase II pausing, whereas 5‐methylcytosine evicts CTCF, leading to exon exclusion. However, the mechanisms governing dynamic DNA methylation at CTCF‐binding sites were unclear. Here, we reveal the methylcytosine dioxygenases TET1 and TET2 as active regulators of CTCF‐mediated alternative splicing through conversion of 5‐methylcytosine to its oxidation derivatives. 5‐hydroxymethylcytosine and 5‐carboxylcytosine are enriched at an intragenic CTCF‐binding sites in the CD45 model gene and are associated with alternative exon inclusion. Reduced TET levels culminate in increased 5‐methylcytosine, resulting in CTCF eviction and exon exclusion. In vitro analyses establish the oxidation derivatives are not sufficient to stimulate splicing, but efficiently promote CTCF association. We further show genomewide that reciprocal exchange of 5‐hydroxymethylcytosine and 5‐methylcytosine at downstream CTCF‐binding sites is a general feature of alternative splicing in naïve and activated CD4+ T cells. These findings significantly expand our current concept of the pre‐mRNA “splicing code” to include dynamic intragenic DNA methylation catalyzed by the TET proteins.
68 SHORTLEAF PINE : A SPECIES AT RISK ?

1Professor (CGT), Department of Natural Resource Ecology and Management, Oklahoma State University, Stillwater, OK 74078; PhD student (SX), Department of Natural Resource Ecology and Management, Oklahoma State University, Stillwater, OK 74078; Research Geneticist and Project Leader (CDN), Southern Institute of Forest Genetics, USDA Forest Service, Saucier, MS 39574, Supervisory Ecologist and Project Leader (JMG), Southern Research Station, USDA Forest Service, P.O. Box 1270, Hot Springs, AR 71902. CGT is corresponding author: to contact, call (405) 744-5462 or email at chuck.tauer@okstate.edu ABSTRACT. —Since the 1950s the existence of natural hybrids between shortleaf pine and loblolly pine has been recognized and reported in the literature. In a range-wide study of isoenzyme diversity in shortleaf pine, we found 16 percent of the trees from western populations were hybrids, based on the isocitrate dehydrogenase (IDH) locus. In stands thought to be pure shortleaf pine in west central Arkansas (Mt. Ida), we found 15 percent of the trees were hybrid. As a follow-up study to confi rm or discount these results, we sampled native stands across Montgomery County, Arkansas, including the Mt. Ida area. These stands were mixed loblolly pine and shortleaf pine in the southeast part of the county and pure shortleaf pine in the northwest corner. In these stands we again found (1) a relatively high percentage of hybrid trees (14 percent); (2) hybrids in shortleaf pine stands beyond the natural range of loblolly pine; (3) introgression occurring in both directions; and (4) the IDH locus a reliable marker for species and hybrid determination. We are now engaged in a range-wide study of both loblolly pine and shortleaf pine to examine the cause and consequences of natural hybridization between these two species.
Joint inversion of gravity and arrival time data from Parkfield: New constraints on structure and hypocenter locations near the SAFOD drill site

Taking advantage of large datasets of both gravity and elastic wave arrival time observations available for the Parkfield, California region, we generated an image consistent with both types of data. Among a variety of strategies, the best result was obtained from a simultaneous inversion with a stability requirement that encouraged the perturbed model to remain close to a starting model consisting of a best fit to the arrival time data. The preferred model looks essentially the same as the best‐fit arrival time model in areas where ray coverage is dense, with differences being greatest at shallow depths and near the edges of the model where ray paths are few. Earthquake locations change by no more than about 100 m, the general effect being migration of the seismic zone to the northeast, closer to the surface trace of the San Andreas Fault.
Default taxonomy: Ernst Mayr's view of the microbial world.

This perspective is a response to a taxonomic proposal by E. Mayr ["Two empires or three? " (1998) Proc. Natl. Acad. Sci. USA 95, 9720-9723]. Mayr has suggested that the now accepted classification of life into three primary domains, Archaea, Bacteria, and Eucarya-originally proposed by myself and others--be abandoned in favor of the earlier Prokaryote-Eukaryote classification. Although the matter appears a taxonomic quibble, it is not that simple. At issue here are differing views as to the nature of biological classification, which are underlain by differing views as to what biology is and will be--matters of concern to all biologists.
RCMC

During the past few years, the analysis of data generated from Location-Based Social Networks (LBSNs) have aided in the identification of urban patterns, understanding activity behaviours in urban areas, as well as producing novel recommender systems that facilitate users’ choices. Recognizing crowd-mobility patterns in cities is very important for public safety, traffic managment, disaster management, and urban planning. In this article, we propose a framework for Recognizing the Crowd Mobility Patterns in Cities using LBSN data. Our proposed framework comprises four main components: data gathering, recurrent crowd-mobility patterns extraction, temporal functional regions detection, and visualization component. More specifically, we employ a novel approach based on Non-negative Matrix Factorization and Gaussian Kernel Density Estimation for extracting the recurrent crowd-mobility patterns in cities illustrating how crowd shifts from one area to another during each day across various time slots. Moreover, the framework employs a hierarchical clustering-based algorithm for identifying what we refer to as temporal functional regions by modeling functional areas taking into account temporal variation by means of check-ins’ categories. We build the framework using a spatial-temporal dataset crawled from Twitter for two entire years (2013 and 2014) for the area of Manhattan in New York City. We perform a detailed analysis of the extracted crowd patterns with an exploratory visualization showing that our proposed approach can identify clearly obvious mobility patterns that recur over time and location in the urban scenario. Using same time interval, we show that correlating the temporal functional regions with the recognized recurrent crowd-mobility patterns can yield to a deeper understanding of city dynamics and the motivation behind the crowd mobility. We are confident that our proposed framework not only can help in managing complex city environments and better allocation of resources based on the expected crowd mobility and temporal functional regions but also can have a direct implication on a variety of applications such as personalized recommender systems, anomalous event detection, disaster resilience management systems, and others.
Clinical course and predictive value of congestion during hospitalization in patients admitted for worsening signs and symptoms of heart failure with reduced ejection fraction: findings from the EVEREST trial.

AIMS Signs and symptoms of congestion are the most common cause for hospitalization for heart failure (HHF). The clinical course and prognostic value of congestion during HHF has not been systemically characterized. METHODS AND RESULTS A post hoc analysis was performed of the placebo group (n = 2061) of the EVEREST trial, which enrolled patients within 48 h of admission (median ~24 h) for worsening HF with an EF ≤ 40% and two or more signs or symptoms of fluid overload [dyspnoea, oedema, or jugular venous distension (JVD)] for a median follow-up of 9.9 months. Clinician-investigators assessed patients daily for dyspnoea, orthopnoea, fatigue, rales, pedal oedema, and JVD and rated signs and symptoms on a standardized 4-point scale ranging from 0 to 3. A modified composite congestion score (CCS) was calculated by summing the individual scores for orthopnoea, JVD, and pedal oedema. Endpoints were HHF, all-cause mortality (ACM), and ACM + HHF. Multivariable Cox regression models were used to evaluate the risk of CCS at discharge on outcomes at 30 days and for the entire follow-up period. The mean CCS obtained after initial therapy decreased from the mean ± SD of 4.07 ± 1.84 and the median (25th, 75th) of 4 (3, 5) at baseline to 1.11 ± 1.42 and 1 (0, 2) at discharge. At discharge, nearly three-quarters of study participants had a CCS of 0 or 1 and fewer than 10% of patients had a CCS >3. B-type natriuretic peptide (BNP) and amino terminal-proBNP, respectively, decreased from 734 (313, 1523) pg/mL and 4857 (2251, 9642) pg/mL at baseline to 477 (199, 1079) pg/mL, and 2834 (1218, 6075) pg/mL at discharge/Day 7. A CCS at discharge was associated with increased risk (HR/point CCS, 95% CI) for a subset of endpoints at 30 days (HHF: 1.06, 0.95-1.19; ACM: 1.34, 1.14-1.58; and ACM + HHF: 1.13, 1.03-1.25) and all outcomes for the overall study period (HHF: 1.07, 1.01-1.14; ACM: 1.16, 1.09-1.24; and ACM + HHF 1.11, 1.06-1.17). Patients with a CCS of 0 at discharge experienced HHF of 26.2% and ACM of 19.1% during the follow-up. CONCLUSION Among patients admitted for worsening signs and symptoms of HF and reduced EF, congestion improves substantially during hospitalization in response to standard therapy alone. However, patients with absent or minimal resting signs and symptoms at discharge still experienced a high mortality and readmission rate.
Microbiological and molecular characterization of human clinical isolates of Staphylococcus cohnii, Staphylococcus hominis, and Staphylococcus sciuri

Abstract Background: The incidence of coagulase-negative staphylococci reported as causative agents of nosocomial infections has risen in the last decade. The aim of this study was to characterize biofilm formation, antibiotic resistance, SCCmec type, and genetic relatedness in clinical isolates of Staphylococcus cohnii, Staphylococcus hominis, and Staphylococcus sciuri recovered from humans. Methods: Clinically relevant isolates of S. cohnii (n = 15), S. hominis (n = 9), and S. sciuri (n = 6), were collected from patients. Biofilm formation was evaluated using crystal violet staining, drug susceptibility was assessed using the broth microdilution method, and methicillin resistance was measured using the cefoxitin disk test. SCCmec was typed using 2 different methodologies, and genetic relatedness was determined by pulsed-field gel electrophoresis (PFGE). Results: Sixty percent (9/15) of S. cohnii, 33% (3/9) of S. hominis, and 50% (3/6) of S. sciuri isolates were categorized as weak producers of biofilm. None of the isolates were resistant to vancomycin or linezolid. All 3 species showed a high resistance (> 66%) to ampicillin, levofloxacin, erythromycin, and ceftriaxone, and the majority of the isolates were methicillin-resistant. PFGE revealed that the S. cohnii isolates comprised 1 dominant clone. Conclusions: The S. cohnii, S. hominis, and S. sciuri isolates analyzed in this study showed a high methicillin resistance and resistance to other antimicrobials. The results of this study strongly suggest that coagulase-negative staphylococci harbour new SCCmec elements. We report the first case of a clone of S. cohnii associated with human disease.
Decreased Expression of Bioinformatically Predicted piwil2-targetting microRNAs, miR-1267 and miR-2276 in Breast Cancer.

PURPOSE Human Piwil2, a member of Piwi subfamily of Argonaute proteins, is primarily expressed in testis, where it regulates self-renewal of germ cells. However, its ectopic expression has been reported with several tumors, including breast cancer. The upregulation of piwil2 in various stages of breast cancer suggested its suitability as a novel tumor biomarker. Considering the vital role of microRNAs (miRNAs) in regulating the expression of most human genes, we hypothesized a concomitant downregulation of the bioinformatically-predicted piwil2-targetting microRNAs in breast cancer. METHOD We employed different bioinformatic tools to predict piwil2-targeting miRNAs. Then, from the list of predicted miRNAs, we chose two less studied miRNAs (miR-1267 and miR-2276) for experimental validation. Using a real-time RT-PCR approach, we quantified the relative expression of the miRNAs in 31 pairs of formalin-fixed paraffin-embedded tumor/non-tumor tissue samples. RESULTS Our data revealed a noticeable but not statistically significant (P = 0.133) downregulation of miR-1267 in tumor samples, compared to non-tumor samples obtained from the same patients. Downregulation of miR-1267 was more significant in higher grades of malignancies (fold change = 2.39, P = 0.033) and also in lymph nodes containing high-grade tumor cells (fold change = 6.66, P = 0.02). Interestingly, a significant upregulation of miR-1267 was observed in tumors at high stages (stage 3a, 3b), compared to low stages (stage 2a, 2b) (fold change = 8.05, P = 0.048). Similar patterns of expression alteration were also observed for miR-2276. CONCLUSION Altogether, our findings suggest a probable tumor suppressor role for miR-1267 and miR-2276 in breast tumor initiation and progression, but a probable promoting role for them in invasion and metastasis.
Deplacement et instabilites de fluides miscibles et immiscibles en cellule de hele-shaw

Ce memoire presente une etude experimentale du deplacement de fluides en cellule de hele-shaw (deux plaques separees par une faible epaisseur). Dans la premiere partie, nous etudions la destabilisation du doigt de saffman-taylor en secteur angulaire observe pour des fluides non miscibles. Nous montrons que la forme de la ligne centrale (fjord) qui divise le doigt en deux branches secondaires est semblable a la trajectoire d'une particule advectee sur l'interface d'un doigt qui resterait stable. Ces fjords se comportent comme des murs virtuels entre lesquels de nouvelles branches secondaires se developpent de sorte que le motif se complexifie rapidement. Nous avons calcule la fonction de distribution de la taille des branches secondaires. Les resultats, en accord avec les observations experimentales, montrent que, en canal lineaire, la probabilite d'observer une branche de taille superieure a la largeur du canal est negligeable. Dans les secteurs de tres grands angles, on observe la formation de fjords infinis separant des structures de grande taille. La seconde partie de ce memoire est consacree a l'etude du deplacement de fluides miscibles en cellule rectangulaire verticale dans la limite des grands nombres de peclet (diffusion negligeable) et en gravite stabilisante. Il se forme alors une mince langue de fluide injecte entre les plaques de la cellule. L'avancee et l'epaisseur de cette langue sont mesurees par absorption de la lumiere. Nous presentons un modele, confirme par les experiences, qui prevoit l'existence de trois domaines differents en fonction des valeurs des parametres de controle. Le premier correspond a une interface dont la forme est celle d'une langue autosimilaire. Le second domaine est marque par la presence d'une pointe de faible diametre. Le troisieme domaine correspond a la formation d'un motif de digitation a trois dimensions, de longueur d'onde egale a cinq fois l'epaisseur de la cellule.
Association between neurovascular contact and clinical characteristics in classical trigeminal neuralgia: A prospective clinical study using 3.0 Tesla MRI

Background Previous studies demonstrated that a severe neurovascular contact (NVC) causing displacement or atrophy of the trigeminal nerve is highly associated with classical trigeminal neuralgia (TN). There are no studies describing the association between the clinical characteristics of TN and severe NVC. Methods Clinical characteristics were prospectively collected from consecutive TN patients using semi-structured interviews in a cross-sectional study design. We evaluated 3.0 Tesla MRI blinded to the symptomatic side. Results We included 135 TN patients. Severe NVC was more prevalent in men (75%) compared to women (38%) (p < 0.001), and the odds in favor of severe NVC on the symptomatic side were 5.1 times higher in men compared to women (95% CI 2.3–10.9, p < 0.001). There was no difference between patients with and without severe NVC in age (≥60 years vs. <60) (OR 1.6 95% CI (0.8–3.4), p = 0.199) or duration of disease (p = 0.101). Conclusions Severe NVC was much more prevalent in men than in women, who may more often have other disease etiologies causing or contributing to TN. Severe NVC was not associated with age or with duration of disease.
Posttraumatic stress disorder after severe traumatic brain injury.

OBJECTIVE This study indexed the profile of posttraumatic stress disorder (PTSD) after severe traumatic injury to the brain. METHOD Patients who sustained a severe traumatic brain injury (N=96) were assessed for PTSD 6 months after the injury with the PTSD Interview, a structured clinical interview based on DSM-III-R criteria. RESULTS PTSD was diagnosed in 26 (27.1%) of the patients. While only 19.2% (N=5) of the patients with PTSD reported intrusive memories of the trauma, 96.2% (N=25) reported emotional reactivity. Intrusive memories, nightmares, and emotional reactivity had very strong positive predictive values for the presence of PTSD. CONCLUSIONS These findings indicate that PTSD can develop after severe traumatic brain injury. The predominance of emotional reactivity and the relative absence of traumatic memories in patients with PTSD who suffered impaired consciousness during trauma suggest that traumatic experiences can mediate PTSD at an implicit level.
Infrared and red PPG signals analysis of the healthy subjects and clinical patients

A lab-made photoplethysmographic (PPG) device was applied to measure PPG signals of healthy cohorts and selected patients by medical doctors for arterial elasticity assessment. The off-line analysis on vascular health was done afterwards using a commercial software. The received information is repeatable and reproducible, however, sometimes not unambiguous. Temporal parameters of the signal components were studied in order to define the invariants by means of optimal envelope construction. After PPG pulse series normalization the series were twice differentiated and the maxima (A) and minima (B) of the second order derivative PPGs (SDPPG) were determined. The constructed graphs of the ratios B/A as a function of time were produced for the healthy compared with the vascular patients. Also principal component analysis (PCA) was used in decomposing the PPG signal for finding functional relationships between components. The 30-points moving averages were calculated for B/A value series of each SDPPG signals which is presented as the result. The B/A index shows higher values for the finger arteries compared the toe arteries. The infrared based B/A index values were higher than the red based B/A index values, and finger B/A index values were higher than toe B/A index values. The main goal for this study the noninvasive method for arterial elasticity assessment based on clinical and volunteer measurements with PPG & SDPPG means.
Maxillary sinus perforation with presence of an antral pseudocyst, repaired with platelet rich fibrin

The maxillary sinus lifting procedure is an important preprosthetic surgical procedure for the creation of adequate bone volume in the edentulous posterior maxilla for the placement of dental implants. The presence of a maxillary sinus cyst has been considered a contraindication for this operation. Perforation of the membrane and hence the elongation of the healing time for implant placement is the most common complication in this type of procedure. The purpose of the case is to show the safely repair of the large sinus perforation during the sinus lifting with presence of the antral pseudocyst. In this case, we present a patient who had a maxillary sinus lifting procedure in the presence of antral pseudocysts. No complications were seen during follow-up periods and all implants are functioning successfully. Platelet-rich fibrin may be used safely when large perforation occurs during the sinus lifting with the presence of an antral pseudocyst.