Miracle-dz/UniFAR-FTUs huggingface dataset:
Influence of hospital admission in the pharmacotherapy complexity of HIV+ patients.

OBJECTIVE To determine the variation in the pharmacotherapy complexity index in HIV+ patients after hospital admission. METHOD A retrospective, single-center study with HIV+ patients on antiretroviral treatment (ART) who were admitted to hospital between 2008 and 2015 were conducted. Demographic, analytical, clinical and pharmacotherapy variables were collected, as well as those about the use of healthcare resources. The primary endpoint was the variation in the overall complexity index after a hospital admission, measured through the MRCI tool (University of Colorado). There was also an analysis of the variation in adherence to ART, and of the causes that led to an increase in pharmacotherapy complexity after hospitalization. RESULTS The study included 146 patients (84.9% male) with 45.3 ± 9.1 years as mean age; 30.8% of these patients had experienced an admission to hospital in the previous year, with a median stay of seven days (IQR: 4-12,5). The mean overall complexity before hospital admission was 14.5 ± 7.2 vs. 16.5 ± 8.0 after admission, with a significant difference (1.97 [CI = 0.85;3.09]). The percentage of patients adherent to ART before admission was 58.3% vs. 41.8% after admission (p = 0.023). The only factor associated to an increase in complexity was having five or more chronic drugs prescribed before admission (OR = 3.146 [1.045-9.471]). CONCLUSION The overall pharmacotherapy complexity increased after hospital admission, reducing the adherence to ART. Chronic treatment prescribed before admission was the only factor associated with an increase in complexity after admission.
Using arm and hand gestures to command robots during stealth operations

Command of support robots by the warfighter requires intuitive interfaces to quickly communicate high degree-offreedom (DOF) information while leaving the hands unencumbered. Stealth operations rule out voice commands and vision-based gesture interpretation techniques, as they often entail silent operations at night or in other low visibility conditions. Targeted at using bio-signal inputs to set navigation and manipulation goals for the robot (say, simply by pointing), we developed a system based on an electromyography (EMG) "BioSleeve", a high density sensor array for robust, practical signal collection from forearm muscles. The EMG sensor array data is fused with inertial measurement unit (IMU) data. This paper describes the BioSleeve system and presents initial results of decoding robot commands from the EMG and IMU data using a BioSleeve prototype with up to sixteen bipolar surface EMG sensors. The BioSleeve is demonstrated on the recognition of static hand positions (e.g. palm facing front, fingers upwards) and on dynamic gestures (e.g. hand wave). In preliminary experiments, over 90% correct recognition was achieved on five static and nine dynamic gestures. We use the BioSleeve to control a team of five LANdroid robots in individual and group/squad behaviors. We define a gesture composition mechanism that allows the specification of complex robot behaviors with only a small vocabulary of gestures/commands, and we illustrate it with a set of complex orders.
Discovery of Benzimidazole–Quinolone Hybrids as New Cleaving Agents toward Drug‐Resistant Pseudomonas aeruginosa DNA

A series of benzimidazole–quinolone hybrids as new potential antimicrobial agents were designed and synthesized. Bioactive assays indicated that some of the prepared compounds exhibited potent antibacterial and antifungal activities. Notably, 2‐fluorobenzyl derivative 5 b (ethyl 7‐chloro‐6‐fluoro‐1‐[[1‐[(2‐fluorophenyl)methyl]benzimidazol‐2‐yl]methyl]‐4‐oxo‐quinoline‐3‐carboxylate) showed remarkable antimicrobial activity against resistant Pseudomonas aeruginosa and Candida tropicalis isolated from infected patients. Active molecule 5 b could not only rapidly kill the tested strains, but also exhibit low toxicity toward Hep‐2 cells. It was more difficult to trigger the development of bacterial resistance of P. aeruginosa against 5 b than that against norfloxacin. Molecular docking demonstrated that 5 b could effectively bind with topoisomerase IV–DNA complexes, and quantum chemical studies theoretically elucidated the good antimicrobial activity of compound 5 b. Preliminary experimental reaction mechanism exploration suggested that derivative 5 b could not intercalate into DNA isolated from drug‐resistant P. aeruginosa, but was able to cleave DNA effectively, which might further block DNA replication to exert powerful bioactivities. In addition, compound 5 b is a promising antibacterial agent with membrane disruption abilities.
Orthotopic Transplantation of Achilles Tendon Allograft in Rats

The biology and function of orthotopic transplantation of Achilles tendon allograft are unknown. Particularly, the revitalization of Achilles allograft is a clinical concern. Achilles allografts were harvested from donor rats and stored at −80 °C. Subcutaneous adipose tissue was harvested from the would-be allograft recipient rats for isolation of mesenchymal stem cells (MSCs). MSCs were cultured with growth differentiation factor-5 (GDF-5) and applied onto Achilles allografts on the day of transplantation. After the native Achilles tendon was resected from the left hind limb of the rats, Achilles allograft, with or without autologous MSCs, was implanted and sutured with calf muscles proximally and calcaneus distally. Animal gait was recorded presurgery and postsurgery weekly. The animals were sacrificed at week 4, and the transplanted Achilles allografts were collected for biomechanical testing and histology. The operated limbs had altered gait. By week 4, the paw print intensity, stance time, and duty cycle (percentage of the stance phase in a step cycle) of the reconstructed limbs were mostly recovered to the baselines recorded before surgery. Maximum load of failure was not different between Achilles allografts, with or without MSCs, and the native tendons. The Achilles allograft supplemented with MSCs had higher cellularity than the Achilles allograft without MSCs. Deposition of fine collagen (type III) fibers was active in Achilles allograft, with or without MSCs, but it was more evenly distributed in the allografts that were incubated with MSCs. In conclusion, orthotopically transplanted Achilles allograft healed with host tissues, regained strength, and largely restored Achilles function in 4 wk in rats. It is therefore a viable option for the reconstruction of a large Achilles tendon defect. Supplementation of MSCs improved repopulation of Achilles allograft, but large animal models, with long-term follow up and cell tracking, may be required to fully appreciate the functional benefits of MSCs.
Imaging of Big and Messy Biological Structures Using Electron Tomography

Any student of cell biology cannot help but be impressed with the exquisite organization of cellular and subcellular compartments, where Individual proteins and even nucleic acids are targeted to specific domains and held together in macromolecular assemblies to achieve orderly and efficient interactions. Perhaps nowhere is the specialization of cellular compartments more apparent than in the nervous system, where the cell contains multiple, well-defined functional domains, each with its own unique biochemical character.
Investigations of the microbial diversity and dynamics in activated sludge using molecular methods

Wastewater treatment is necessary to reduce the health risks and environmental impacts associated with discharge of untreated wastewater. The most common way to treat wastewater in wastewater treatment plants is through the activated sludge process. Although the main principle of the process has been the same since its usage began 100 years ago, there has been a continuous development and modern wastewater treatment plants can be designed to remove not only organic material but also nitrogen and phosphorus by exploiting the properties of different microorganisms. However, as the demands on the wastewater treatment plants are increasing, either by lowered accepted effluent concentrations of nutrients or by increased volumes of wastewater, there is a need for further development of the processes. For this development to be possible, an increased understanding of the factors governing the composition and dynamics of the microbial communities in the wastewater treatment plants, is regarded as fundamental. The research presented in this thesis focused on the investigation of the diversity and dynamics of the microbial community in the activated sludge of a large wastewater treatment plant. Novel tools and methods for the analysis of data from a DNA-fingerprinting method, terminal restriction fragment polymorphism analysis, were developed and used for longitudinal studies of Bacteria and Archaea in the activated sludge. The archaeal community was determined to be less diverse, present in lower numbers and more static than the bacterial community. Methanogens, likely entering the sludge with the recycled water from an anaerobic bioreactor, dominated the archaeal community. The most abundant bacterial classes were the Alphaproteobacteria and Betaproteobacteria, which are both commonly found in varying proportions in wastewater treatment plants. However, which of these two phyla that was the most abundant, was found to be highly dependent on the method used to describe the diversity. Seasonal variations in the bacterial community composition were observed and could be explained by the seasonal variations in temperature. A major operational change, by-passing of the primary settlers due to maintenance work, also coincided with changes in community composition. Thus, both operational parameters, such as treatment plant design, and environmental parameters which cannot be controlled, such as temperature, appear to be shaping the bacterial community in the activated sludge. Changes in both the archaeal and bacterial community composition coincided with observed changes in activated sludge floc properties. However, further studies are required to determine if these observations were due to causal relationships.
Confirmation of Glyphosate-Resistant Horseweed (Conyza canadensis) in Montana Cereal Production and Response to POST Herbicides

In recent years, horseweed has become an increasing problem in Montana. To confirm and characterize the level of glyphosate resistance, seeds were collected from putative glyphosate-resistant (GR) horseweed (GR-MT) plants in a wheat—fallow field in McCone County, MT. Known GR (GR-NE) and glyphosate-susceptible (GS-NE) horseweed accessions from Lincoln, NE, were included for comparison in dose—response and shikimate accumulation studies. Whole-plant glyphosate dose—response experiments conducted at the early- (5- to 8-cm diameter) and late- (12- to 15-cm diameter) rosette stages of horseweed indicated that GR-MT accessions had a 2.5- to 4.0-fold level of resistance to glyphosate relative to the GS-NE accession, on the basis of shoot dry weight (GR50 values). The level of resistance was 3.1- to 7.9-fold on the basis of visually assessed injury estimates (I50 values). At the whole-plant level, about 2.1- to 4.5-fold higher shikimate accumulation was observed in the GS-NE accession compared with the GR-MT and GR-NE accessions over a 10-d period after glyphosate was applied at 1,260 g ae ha-1. In a separate greenhouse study, all three horseweed accessions were also screened with alternate POST herbicides registered for use in wheat—fallow rotations. The majority of the tested herbicides provided ≥90% injury at the field-use rates for all three horseweed accessions 3 wk after treatment. This is the first published report on the occurrence of GR horseweed in Montana cereal production. Increased awareness and adoption of best management practices, including the use of diversified (based on multiple sites of action) herbicide programs highlighted in this study, would aid in mitigating the further spread of GR horseweed in the cereal production fields of the U.S. Great Plains. Nomenclature: Glyphosate; horseweed, Conyza canadensis (L.) Cronq. ; wheat, Triticum aestivum L.
Microaneurysm detection with radon transform-based classification on retina images

The creation of an automatic diabetic retinopathy screening system using retina cameras is currently receiving considerable interest in the medical imaging community. The detection of microaneurysms is a key element in this effort. In this work, we propose a new microaneurysms segmentation technique based on a novel application of the radon transform, which is able to identify these lesions without any previous knowledge of the retina morphological features and with minimal image preprocessing. The algorithm has been evaluated on the Retinopathy Online Challenge public dataset, and its performance compares with the best current techniques. The performance is particularly good at low false positive ratios, which makes it an ideal candidate for diabetic retinopathy screening systems.
Hydrophilic Polymer Embolism: Implications for Manufacturing, Regulation, and Postmarket Surveillance of Coated Intravascular Medical Devices

Supplemental digital content is available in the text. Abstract Hydrophilic polymers are ubiquitously applied as surface coatings on catheters and intravascular medical technologies. Recent clinical literature has heightened awareness on the complication of hydrophilic polymer embolism, the phenomenon wherein polymer coating layers separate from catheter and device surfaces, and may be affiliated with a range of unanticipated adverse reactions. Significant system barriers have limited and delayed reporting on this iatrogenic complication, the full effects of which remain underrecognized by healthcare providers and manufacturers of various branded devices. In 2015, the United States Food and Drug Administration acknowledged rising clinical concerns and stated that the agency would work with stakeholders to further evaluate gaps that exist in current national and international device standards for coated intravascular medical technologies. The present article reviews current knowledge on this complication as well as factors that played a role in delaying detection and dissemination of information and new knowledge once hazards and clinical risks were identified. Furthermore, organ-specific effects and adverse reaction patterns are summarized, along with implications for device manufacturing, safety assurance, and regulation. Qualitative and quantitative particulate testing are needed to optimize coated intravascular device technologies. Moreover, general enhanced processes for medical device surveillance are required for timely adverse event management and to ensure patient safety.
The Developmental Trajectory of Imitation in Infants with Autism Spectrum Disorders: A Prospective Study

Impairments in imitation are present in young children with autism spectrum disorders (ASD), but the onset of these impairments is unknown. The present study investigated the developmental trajectories affiliated with various types of imitation. Imitative performances in infancy were observed in a prospective design, and retrospectively compared between ASD and typically developing (TD) infants. The results indicated that infants who later presented the symptoms of ASD showed less imitation at 13 months of age, but not at 11 months. Both of TD and ASD infants imitated more object manipulations than gestures and meaningless movements, and gestures were more frequent than meaningless movements. Imitation impairments in ASD appear to be delayed instead of being atypical. Our findings can be used in assessments of ASD before 18 months of age.
DISP: Optimizations towards Scalable MPI Startup

Despite the popularity of MPI for high performance computing, the startup of MPI programs faces a scalability challenge as both the execution time and memory consumption increase drastically at scale. We have examined this problem using the collective modules of Cheetah and Tuned in Open MPI as representative implementations. Previous improvements for collectives have focused on algorithmic advances and hardware off-load. In this paper, we examine the startup cost of the collective module within a communicator and explore various techniques to improve its efficiency and scalability. Accordingly, we have developed a new scalable startup scheme with three internal techniques, namely Delayed Initialization, Module Sharing and Prediction-based Topology Setup (DISP). Our DISP scheme greatly benefits the collective initialization of the Cheetah module. At the same time, it helps boost the performance of non-collective initialization in the Tuned module. We evaluate the performance of our implementation on Titan supercomputer at ORNL with up to 4096 processes. The results show that our delayed initialization can speed up the startup of Tuned and Cheetah by an average of 32.0% and 29.2%, respectively, our module sharing can reduce the memory consumption of Tuned and Cheetah by up to 24.1% and 83.5%, respectively, and our prediction-based topology setup can speed up the startup of Cheetah by up to 80%.
Origins and spread of fluted-point technology in the Canadian Ice-Free Corridor and eastern Beringia

Significance We report geometric morphometric and cladistic analyses of archaeological materials establishing early human interaction between the North American Arctic, western Canadian “Ice-Free Corridor,” and temperate North America prior to 12,000 years ago, when the Corridor is inferred to have opened after initial retreat of the continental ice sheets. The findings inform a broad range of scientists engaged in genomic, evolutionary, ecological, climatological, geological, and anthropological studies of the late Pleistocene, providing tangible evidence of human dispersal through the Americas and placing the archaeological record in the context of new genetic models chronicling the initial migration into America, as well as paleoecological interpretations of the “opening” of interior western Canada’s earliest habitable environments. Fluted projectile points have long been recognized as the archaeological signature of early humans dispersing throughout the Western Hemisphere; however, we still lack a clear understanding of their appearance in the interior “Ice-Free Corridor” of western Canada and eastern Beringia. To solve this problem, we conducted a geometric morphometric shape analysis and a phylogenetic analysis of technological traits on fluted points from the archaeological records of northern Alaska and Yukon, in combination with artifacts from further south in Canada, the Great Plains, and eastern United States to investigate the plausibility of historical relatedness and evolutionary patterns in the spread of fluted-point technology in the latest Pleistocene and earliest Holocene. Results link morphologies and technologies of Clovis, certain western Canadian, and northern fluted points, suggesting that fluting technology arrived in the Arctic from a proximate source in the interior Ice-Free Corridor and ultimately from the earliest populations in temperate North America, complementing new genomic models explaining the peopling of the Americas.
Pressure Boundaries for Implicit Incompressible

Implicit incompressible SPH (IISPH) solves a pressure Poisson equation (PPE). While the solution of the PPE provides pressure at fluid samples, the embedded boundary handling does not compute pressure at boundary samples. Instead, IISPH uses various approximations to remedy this deficiency. In this paper, we illustrate the issues of these IISPH approximations. We particularly derive Pressure Boundaries, a novel boundary handling that overcomes previous IISPH issues by the computation of physically meaningful pressure values at boundary samples. This is basically achieved with an extended PPE. We provide a detailed description of the approach that focuses on additional technical challenges due to the incorporation of boundary samples into the PPE. We therefore use volume-centric SPH discretizations instead of typically used density-centric ones. We further analyze the properties of the proposed boundary handling and compare it to the previous IISPH boundary handling. In addition to the fact that the proposed boundary handling provides physically meaningful pressure and pressure gradients at boundary samples, we show further benefits such as reduced pressure oscillations, improved solver convergence and larger possible time steps. The memory footprint of fluid samples is reduced and performance gain factors of up to five compared to IISPH are presented.
Lamina Cribrosa Changes after Laser In Situ Keratomileusis in Myopic Eyes

Purpose To determine deep optic nerve head structure changes after transient intraocular pressure elevation during laser in situ keratomileusis (LASIK) for myopia. Methods Enhanced depth imaging-optical coherence tomography was performed in each myopic eye that underwent LASIK surgery. Enhanced depth imaging-optical coherence tomography images were created at postoperative 1 day, 1 week, 2 weeks, and 1 month. Lamina cribrosa (LC) thickness, LC depth and prelaminar thickness at the superior, middle and inferior portions of the optic nerve head were measured by two investigators. Results Forty eyes in 40 patients were included in the present study. During follow-up, there were no significant differences in prelaminar thickness or LC depth. The LC demonstrated increased thickness at postoperative 1 day at all three locations (superior, middle, and inferior) (p < 0.001, p < 0.001, p < 0.001, respectively). However, no significant changes were observed at postoperative 1 week, 2 weeks, and 1 month. Conclusions The LC thickness could increase at 1 day after LASIK surgery. However, the thickness will gradually return to baseline morphology. Temporary intraocular pressure increase during LASIK does not appear to induce irreversible LC thickness changes.
Role of TNF–TNF Receptor 2 Signal in Regulatory T Cells and Its Therapeutic Implications

Tumor necrosis factor α (TNFα) is a pleiotropic cytokine which signals through TNF receptor 1 (TNFR1) and TNF receptor 2 (TNFR2). Emerging evidence has demonstrated that TNFR1 is ubiquitously expressed on almost all cells, while TNFR2 exhibits a limited expression, predominantly on regulatory T cells (Tregs). In addition, the signaling pathway by sTNF via TNFR1 mainly triggers pro-inflammatory pathways, and mTNF binding to TNFR2 usually initiates immune modulation and tissue regeneration. TNFα plays a critical role in upregulation or downregulation of Treg activity. Deficiency in TNFR2 signaling is significant in various autoimmune diseases. An ideal therapeutic strategy for autoimmune diseases would be to selectively block the sTNF/TNFR1 signal through the administration of sTNF inhibitors, or using TNFR1 antagonists while keeping the TNFR2 signaling pathway intact. Another promising strategy would be to rely on TNFR2 agonists which could drive the expansion of Tregs and promote tissue regeneration. Design of these therapeutic strategies targeting the TNFR1 or TNFR2 signaling pathways holds promise for the treatment of diverse inflammatory and degenerative diseases.