Miracle-dz/UniFAR-FTUs huggingface dataset:
Accelerated 4D phase contrast MRI in skeletal muscle contraction

3D time‐resolved (4D) phase contrast MRI can be used to study muscle contraction. However, 3D coverage with sufficient spatiotemporal resolution can only be achieved by interleaved acquisitions during many repetitions of the motion task, resulting in long scan times. The aim of this study was to develop a compressed sensing accelerated 4D phase contrast MRI technique for quantification of velocities and strain rate of the muscles in the lower leg during active plantarflexion/dorsiflexion.
Contact lenses for ophthalmic drug delivery

Contact lenses as a means to deliver pharmaceuticals to the eye have seen a significant increase in research interest in the past few years. This review will detail the in vitro experiments which have investigated use of these contact lenses in the context of the desired pharmacological treatment goals in the management of infectious, inflammatory, allergic and glaucomatous diseases of the eye. The techniques researchers have employed to modify and tailor drug release rates from these materials, including the use of vitamin E diffusion barriers, modified ionicity, molecular imprinting and incorporation of drug reservoirs, will be discussed, as well as their impact on drug release kinetics. Finally, the demonstration of the feasibility of these materials when applied in vivo in animal models as well as in humans with and without disease will be presented and their results discussed relating to their implications for the future of the field.
Management of the frozen shoulder

Frozen shoulder is a very common condition with a prevalence of 2%-5% in the general population. Decrease in joint volume as a result of fibrosis and hyperplasia of the joint capsule leads to painful and restricted glenohumeral motion. Frozen shoulder is a self- limiting disease with a chronic character, and is mostly treated in a primary care setting. In this review, we set out to address the current evidence-based literature on management of this disabling disease using a PubMed search. Many non-surgical and surgical therapeutic options are described, including supervised neglect, intra-articular corticosteroid injections, physical therapy, manipulation under anesthesia, capsular distension, and arthroscopic capsular release. In the literature, the long-term outcome shows a significant decrease in pain and improvement of shoulder function for all treatment modalities without clear evidence of superiority of one over the other. This possibly indicates that a self-limiting character is the most important factor in the course of the disease. Management of frozen shoulder is primarily conservative. Supervised neglect is combined with analgesia and stretching exercises as the pain subsides. In the early painful phase, intra-articular corticosteroid injections are recommended for pain relief. When the patient has persistent pain and glenohumeral stiffness after adequate conservative treatment, invasive options can be considered, like arthroscopic capsular release, manipulation under anesthesia, or capsular distension.
Deregulation of KSHV latency conformation by ER-stress and caspase-dependent RAD21-cleavage

Kaposi’s sarcoma (KS)-associated herpesvirus (KSHV) is a human gammaherpesvirus recognized as the principal causative agent of KS and primary effusion lymphoma (PEL). KSHV establishes persistent latent infection in B lymphocytes where viral gene expression is restricted, in part, by a cohesin-dependent chromosome conformation. Here, we show that endoplasmic reticulum (ER) stress induces a rapid, caspase-dependent cleavage of cohesin subunit RAD21. ER stress-induced cleavage of RAD21 correlated with a rapid and strong viral lytic transcriptional activation. This effect was observed in several KSHV positive PEL cells, but not in other B-cells or non-B-cell models of KSHV latency. The cleaved-RAD21 does not dissociate from viral genomes, nor disassemble from other components of the cohesin complex. However, RAD21 cleavage correlated with the disruption of the latency genome conformation as revealed by chromosome conformation capture (3C). Ectopic expression of C-terminal RAD21 cleaved form could partially induce KSHV lytic genes transcription in BCBLI cells, suggesting that ER-stress induced RAD21 cleavage was sufficient to induce KSHV reactivation from latency in PEL cells. Taken together our results reveal a novel aspect for control and maintenance of KSHV genome latency conformation mediated by stress-induced RAD21 cleavage. Our studies also suggest that RAD21 cleavage may be a general regulatory mechanism for rapid alteration of cellular chromosome conformation and cohesin-dependent transcription regulation.
Nitrogen sediment fluxes in an upwelling system off central Chile (Concepción Bay and adjacent shelf) during the 1997-1998 El Niño

Se analizaron los flujos de compuestos nitrogenados desde los sedimentos en dos areas representativas de condiciones costeras y de plataforma (Bahia Concepcion y plataforma adyacente, respectivamente). Durante el periodo de muestreo las aguas de fondo presentaron un anomalamente alto contenido de oxigeno disuelto, coincidente con el evento El Nino 1997-1998. De ambos sitios, se incubaron testigos de sedimento intactos para determinar los flujos totales de NH4+. Ademas se determino la concentracion de NH4+, NO3- y NO2- en el agua intersticial para estimar los flujos difusivos de compuestos nitrogenados en la interfase agua-sedimento. Los flujos de NH4+ totales variaron entre 0,55 y 2,18 mmol m-2 dia-1 al interior de la bahia y entre 1,84 a 2,14 mmol m-2 dia-1 en la plataforma. Se observaron flujos difusivos de NO3- en direccion a los sedimentos al interior de la bahia en Marzo de 1998 (-17 x 10-2 mmol m-2 dia-1) y en la plataforma en Noviembre de 1997 (-2,7 x 10-2 mmol m-2 dia-1) asociados a los flujos difusivos de NH4+ mas bajos, coincidiendo esto con la mayor gradiente de Eh en los sedimentos superficiales. Ademas, los bajos flujos de NH4+ medidos en comparacion con mediciones previas, sugieren la influencia de un ambiente menos reductor, generado a su vez por la disminucion del flujo de material organico particulado y por el aumento de las concentraciones de oxigeno disuelto en las aguas del fondo. Estas condiciones fueron generadas probablemente por el evento El Nino. Tambien, con relacion a reportes previos se registro un incremento en los coeficientes de irrigacion (DI). Todo esto sugiere que durante este periodo los flujos de otros compuestos nitrogenados podrian haber adquirido relevancia con relacion a los flujos de NH4+
A Randomized Clinical Trial to Study the Effect of Silicone Gel Dressing and Pressure Therapy on Posttraumatic Hypertrophic Scars

To investigate the effect of pressure therapy (PG), silicone gel sheeting (SGS), and combined therapy on the management of posttraumatic hypertrophic scar (HS) using a randomized controlled clinical trial. A total of 104 subjects with HS mostly resulting from burns and scald injuries (63 men and 41 women; average age: 21.8 ± 18.7 years) were recruited from Jiangsu People's First Affiliated Hospital in Nanjing, China. The mean scar formation period was 14.9 ± 30.8 months. All subjects were randomly allocated into four groups, namely the PG, SGS, combined PG and SGS groups, and single-blinded control group for the treatment of 6 months. Standardized scar assessments (pigmentation, vascularity, thickness, pain, and itchiness) were conducted before the intervention, 2, 4, and 6 months of the intervention, and 1 month after completion of the program, respectively, to observe the progress of the treatments. The results showed that the combined therapy seemed to be more effective in improving the thickness of scar after 2 months of intervention (P < .001). After 6 months of intervention, both the combined therapy group and the PG group showed significant improvement in scar thickness. The improvement in scar thickness was most significant in the combined therapy group. SGS was found to be more effective in alleviating the pain and pruritus rather than the scar thickness. This randomized clinical trial has demonstrated the evidence of the effect of combined PG and gel intervention on posttraumatic HS. The PG group showed an improvement in scar thickness too. Further studies are needed to investigate the biomechanical and physiological effect that PG and gel sheeting would exert on the scar tissues.
HealthTalks - A Mobile App to Improve Health Communication and Personal Information Management

A patient»s health literacy has a direct impact on their health, but more than a third of the USA population has "basic" or "below basic" levels of health literacy. An individual»s wellbeing is also affected by the communication with their physician, as the use of technical terminology may hinder the patient»s understanding. A patient»s ability to, later on, recall or retrieve helpful information could reduce these comprehension problems and this can be improved by a good management of personal health information. To help overcome some of these problems, we created HealthTalks, a mobile app that empowers the patients, easing their daily health tasks and self-care ability. It does so by recording the audio of a medical appointment, transcribing its dialogue, giving more information about medical concepts employed, and allowing information associated with medical appointments to be easily managed by the patient. Usability tests were conducted with elderly people, ranging from the icons used to the general user experience. Results were very positive, with users accomplishing most tasks successfully and often with the least amount of clicks. We also evaluated the speech recognition software used, Google Cloud Speech API, reaching an error rate of 12 percent in medical texts.
On Queue-Size Scaling for Input-Queued Switches

We study the optimal scaling of the expected total queue size in an $n\times n$ input-queued switch, as a function of the number of ports $n$ and the load factor $\rho$, which has been conjectured to be $\Theta (n/(1-\rho))$. In a recent work, the validity of this conjecture has been established for the regime where $1-\rho = O(1/n^2)$. In this paper, we make further progress in the direction of this conjecture. We provide a new class of scheduling policies under which the expected total queue size scales as $O(n^{1.5}(1-\rho)^{-1}\log(1/(1-\rho)))$ when $1-\rho = O(1/n)$. This is an improvement over the state of the art; for example, for $\rho = 1 - 1/n$ the best known bound was $O(n^3)$, while ours is $O(n^{2.5}\log n)$.
A Mechano-Activated Cell Reporter System as a Proxy for Flow-Dependent Endothelial Atheroprotection

The vascular endothelium plays a critical role in the health and disease of the cardiovascular system. Importantly, biomechanical stimuli generated by blood flow and sensed by the endothelium constitute important local inputs that are translated into transcriptional programs and functional endothelial phenotypes. Pulsatile, laminar flow, characteristic of regions in the vasculature that are resistant to atherosclerosis, evokes an atheroprotective endothelial phenotype. This atheroprotective phenotype is integrated by the transcription factor Kruppel-like factor-2 (KLF2), and therefore the expression of KLF2 can be used as a proxy for endothelial atheroprotection. Here, we report the generation and characterization of a cellular KLF2 reporter system, based on green fluorescence protein (GFP) expression driven by the human KLF2 promoter. This reporter is induced selectively by an atheroprotective shear stress waveform in human endothelial cells, is regulated by endogenous signaling events, and is activated by the pharmacological inducer of KLF2, simvastatin, in a dose-dependent manner. This reporter system can now be used to probe KLF2 signaling and for the discovery of a novel chemical-biological space capable of acting as the “pharmacomimetics of atheroprotective flow” on the vascular endothelium.
Classification method comparison on Indonesian social media sentiment analysis

Sentiment analysis from social media has turned out to be essential since individuals are normally genuine with their sentiment on giving their perspective. However, in turning social media into a sentiment analysis possess challenges such as comments are usually ambiguous, language barrier problem, slang words, redundant comment, and sentiment classification. This study attempted to distinguish the issues of sentiment classification from Indonesian social media on Jakarta governor election. Several steps are taken to overcome those problems that include preprocessing. The preprocessing strategy used are removing the unrelated tweet, removing URL, deleting duplicate lines, deleting similar lines, removing the unrelated word, removing hashtag, removing Twitter username, removing number in the comment, removing punctuation, checking slang words, and converting the slang word into appropriate word. The preprocessed sentiment is then classified into positive, negative, and neutral. The classification method used in this study are Summation method, Average on Tweet, Average on Tweet with the threshold on objective score, Weighted Average, and Naïve Bayes method. The experimental results show that Naïve Bayes produce the highest precision, highest recall, and highest accuracy for neutral and positive sentiment. But, Naïve Bayes does not produce good results for negative sentiment.
Futility Scaling : High-Associativity Cache Partitioning ( Extended Version )

As shared last level caches are widely used in many-core CMPs to boost system performance, partitioning a large shared cache among multiple concurrently running applications becomes increasingly important in order to reduce destructive interference. However, while recent works start to show the promise of using replacement-based partitioning schemes, such existing schemes either suffer from severe associativity degradation when the number of partitions is high, or lack the ability to precisely partition the whole cache which leads to decreased resource efficiency. In this paper, we propose Futility Scaling (FS), a novel replacement-based cache partitioning scheme that can precisely partition the whole cache while still maintain high associativity even with a large number of partitions. The futility of a cache line represents the uselessness of the line to application performance and can be ranked in different ways by various policies, e.g., LRU and LFU. The idea of FS is to control the size of a partition by properly scaling the futility of its cache lines. We study the properties of FS on both associativity and sizing in an analytical framework, and we present a feedback-based implementation of FS that incurs little overhead in practice. Simulation results show that FS improves performance over previously proposed Vantage and PriSM by up to 6.0% and 13.7%, respectively.
Microbial Contamination in Burn Patients Undergoing Urgent Intubation as Part of Their Early Airway Management

Inhalation injuries occur in approximately one third of all major burns and account for a significant number of deaths in burn patients each year. Previous studies have examined ventilator-associated pneumonia in patients with inhalation injury, but no study to date has evaluated the incidence of bacterial contamination of the airways on admission in patients with inhalation injuries. Because pulmonary complications have been found to cause or directly contribute to mortality in as high as 77% of patients, with combined inhalation injury and thermal injury, early detection of community-acquired pneumonia may significantly alter treatment outcomes. The authors conducted a retrospective review of all burn patients with early intubation and inhalation injury admitted between January 1, 2004 and December 31, 2006 who underwent bronchoscopy with bronchoalveolar lavage (BAL) within 24 hours of admission. Seventy-four consecutive patients fulfilled the inclusion criteria. Age, sex, percentage of total body surface area (%TBSA), presence of alcohol, site of intubation, grade of injury, and BAL results were examined. Analysis revealed a patient population that was 67.6% male, with a 42.0 ± 17.1-year-old mean age, 27.0 ± 24.7 %TBSA average burn, 1.6 ± 1.2 inhalation grade, 17.8 ± 24.4 ventilator days requirement, 27.3 ± 31.4 days of length of stay, and 21.6% mortality. BAL results were grouped into four categories: 1) No growth, 2) Normal flora, 3) <100,000 colony-forming units (cfu), and 4) >100,000 cfu. By this criteria, 13 patients (17.6%) had no growth, 22 (29.7%) had normal flora, 27 (36.5%) had <100,000 cfu, and 12 (16.2%) had >100,000 cfu on the initial BAL. Therefore, 53% grew pathogenic organisms and 16% had >100,000 cfu on BAL with initial bronchoscopy. The predominant organisms were gram-positive cocci, with Streptococcus viridans found in 15 patients (20%), Staphylococcus aureus in eight (11%), and Streptococcus pneumonia in four (6%). Analysis of the patients with the highest bacterial loads revealed that they were 75% female and had a trend toward an increased ventilator requirement and longer length of stay. Patients with combined thermal and inhalation injury requiring urgent intubation have a high incidence of bacterial bronchial contamination. Inhalation injury creates a damaged tracheobronchial mucosa and early intubation provides a portal for bacterial contamination. Further studies with a larger patient population and randomization to treatment and nontreatment of the BAL culture results may show statistically significant differences in ventilator days, length of stay, and mortality.
Vitamin C and Smoke Inhalation Injury

A second potential therapeutic option for the parenchymal damage caused by inhalation injury is systemic administration of intravenous agents. The unique nature of the effects of the burn and smoke on lung physiology and immunology create new opportunities for systemic treatments targeting specific aspects of the response to injury. In addition, systemic therapies could be either isolated or combined with inhalation therapies to achieve optimal clinical response. The two articles in this section of the compendium address different, yet promising, systemic therapies: antithrombin and vitamin C. (J Burn Care Res 2009;30:184-189)
Novel Ciliate Genetic Code Variants Including the Reassignment of All Three Stop Codons to Sense Codons in Condylostoma magnum

mRNA translation in many ciliates utilizes variant genetic codes where stop codons are reassigned to specify amino acids. To characterize the repertoire of ciliate genetic codes, we analyzed ciliate transcriptomes from marine environments. Using codon substitution frequencies in ciliate protein-coding genes and their orthologs, we inferred the genetic codes of 24 ciliate species. Nine did not match genetic code tables currently assigned by NCBI. Surprisingly, we identified a novel genetic code where all three standard stop codons (TAA, TAG, and TGA) specify amino acids in Condylostoma magnum. We provide evidence suggesting that the functions of these codons in C. magnum depend on their location within mRNA. They are decoded as amino acids at internal positions, but specify translation termination when in close proximity to an mRNA 3′ end. The frequency of stop codons in protein coding sequences of closely related Climacostomum virens suggests that it may represent a transitory state.
Sorting Motifs Involved in the Trafficking and Localization of the PIN1 Auxin Efflux Carrier1

Phenylalanine 165 is important for PIN1 endocytosis and its trafficking through the secretory pathway. In contrast with the wealth of recent reports about the function of μ-adaptins and clathrin adaptor protein (AP) complexes, there is very little information about the motifs that determine the sorting of membrane proteins within clathrin-coated vesicles in plants. Here, we investigated putative sorting signals in the large cytosolic loop of the Arabidopsis (Arabidopsis thaliana) PIN-FORMED1 (PIN1) auxin transporter, which are involved in binding μ-adaptins and thus in PIN1 trafficking and localization. We found that Phe-165 and Tyr-280, Tyr-328, and Tyr-394 are involved in the binding of different μ-adaptins in vitro. However, only Phe-165, which binds μA(μ2)- and μD(μ3)-adaptin, was found to be essential for PIN1 trafficking and localization in vivo. The PIN1:GFP-F165A mutant showed reduced endocytosis but also localized to intracellular structures containing several layers of membranes and endoplasmic reticulum (ER) markers, suggesting that they correspond to ER or ER-derived membranes. While PIN1:GFP localized normally in a μA (μ2)-adaptin mutant, it accumulated in big intracellular structures containing LysoTracker in a μD (μ3)-adaptin mutant, consistent with previous results obtained with mutants of other subunits of the AP-3 complex. Our data suggest that Phe-165, through the binding of μA (μ2)- and μD (μ3)-adaptin, is important for PIN1 endocytosis and for PIN1 trafficking along the secretory pathway, respectively.
Spatial distribution of tuberculosis in Manaus and its social determinants, 2008-2013.

SETTING Brazil ranks eighteenth worldwide in annual numbers of new tuberculosis (TB) cases. The municipality of Manaus, Amazonas State, has the highest incidence of TB in Brazil. OBJECTIVE To evaluate the quality of TB epidemiological surveillance, and to describe the spatial distribution pattern of TB incidence in Manaus and its social determinants. DESIGN An ecological study was performed based on secondary data from TB epidemiological surveillance reports. RESULTS An index was developed to classify neighborhoods in terms of the quality of surveillance and suspected underreporting. Based on data from neighborhoods with better surveillance performance, we observed that the average number of residents per room, the unemployment rate and the proportion of households connected to a sewage system were significant predictors of TB incidence. Seven neighborhoods in the south and west of the city had clusters of high TB transmission. CONCLUSION Our results suggest that the association between TB and social vulnerability is obscured by the poor quality of TB surveillance data. We identified priority areas that require immediate TB control interventions and those where local surveillance efforts should be improved, and generated information useful for formulating more effective actions.
Livedoid Dermatitis and Severe Necrosis (Nicolau’s Syndrome) After Intramuscular Hydroxyzine Injection

Nicolau’s syndrome, also called embolica cutis medicamentosa, is characterized by well- circumscribed livedoid dermatitis with aseptic necrosis after intramuscular injection. We report the case of a 45-year-old woman with severe necrosis of the thigh several days after a routine intramuscular injection of hydroxyzine who was transferred to and treated at our Regional Burn Center. Although there has been one case report and numerous voluntarily reported instances of intramuscular hydroxyzine-induced necrosis to the Food and Drug Administration Spontaneous Reporting System, this phenomenon is rare.