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Bioinformatics (Oxford, England) Jun 2023The UNited RESisdue (UNRES) package for coarse-grained simulations, which has recently been optimized to treat large protein systems, has been implemented on Graphical...
SUMMARY
The UNited RESisdue (UNRES) package for coarse-grained simulations, which has recently been optimized to treat large protein systems, has been implemented on Graphical Processor Units (GPUs). An over 100-time speed-up of the GPU code (run on an NVIDIA A100) with respect to the sequential code and an 8.5 speed-up with respect to the parallel Open Multi-Processing (OpenMP) code (run on 32 cores of 2 AMD EPYC 7313 Central Processor Units (CPUs)) has been achieved for large proteins (with size over 10 000 residues). Due to the averaging over the fine-grain degrees of freedom, 1 time unit of UNRES simulations is equivalent to about 1000 time units of laboratory time; therefore, millisecond time scale of large protein systems can be reached with the UNRES-GPU code.
AVAILABILITY AND IMPLEMENTATION
The source code of UNRES-GPU along with the benchmarks used for tests is available at https://projects.task.gda.pl/eurohpcpl-public/unres.
Topics: Protein Conformation; Proteins; Software; Physics
PubMed: 37338530
DOI: 10.1093/bioinformatics/btad391 -
Sensors (Basel, Switzerland) Apr 2023Temperature-controlled closed-loop systems are vital to the transportation of produce. By maintaining specific transportation temperatures and adjusting to environmental...
Temperature-controlled closed-loop systems are vital to the transportation of produce. By maintaining specific transportation temperatures and adjusting to environmental factors, these systems delay decomposition. Wireless sensor networks (WSN) can be used to monitor the temperature levels at different locations within these transportation containers and provide feedback to these systems. However, there are a range of unique challenges in WSN implementations, such as the cost of the hardware, implementation difficulties, and the general ruggedness of the environment. This paper presents the novel results of a real-life application, where a sensor network was implemented to monitor the environmental temperatures at different locations inside commercial temperature-controlled shipping containers. The possibility of predicting one or more locations inside the container in the absence or breakdown of a logger placed in that location is explored using combinatorial input-output settings. A total of 1016 machine learning (ML) models are exhaustively trained, tested, and validated in search of the best model and the best combinations to produce a higher prediction result. The statistical correlations between different loggers and logger combinations are studied to identify a systematic approach to finding the optimal setting and placement of loggers under a cost constraint. Our findings suggest that even under different and incrementally higher cost constraints, one can use empirical approaches such as neural networks to predict temperature variations in a location with an absent or failed logger, within a margin of error comparable to the manufacturer-specified sensor accuracy. In fact, the median test accuracy is 1.02 degrees Fahrenheit when using only a single sensor to predict the remaining locations under the assumptions of critical system failure, and drops to as little as 0.8 and 0.65 degrees Fahrenheit when using one or three more sensors in the prediction algorithm. We also demonstrate that, by using correlation coefficients and time series similarity measurements, one can identify the optimal input-output pairs for the prediction algorithm reliably under most instances. For example, discrete time warping can be used to select the best location to place the sensors with a 92% match between the lowest prediction error and the highest similarity sensor with the rest of the group. The findings of this research can be used for power management in sensor batteries, especially for long transportation routes, by alternating standby modes where the temperature data for the OFF sensors are predicted by the ON sensors.
PubMed: 37177507
DOI: 10.3390/s23094303 -
PloS One 2022This study characterized associations between annually scaled thermal indices and annual heat stress illness (HSI) morbidity outcomes, including heat stroke and heat...
This study characterized associations between annually scaled thermal indices and annual heat stress illness (HSI) morbidity outcomes, including heat stroke and heat exhaustion, among active-duty soldiers at ten Continental U.S. (CONUS) Army installations from 1991 to 2018. We fit negative binomial models for 3 types of HSI morbidity outcomes and annual indices for temperature, heat index, and wet-bulb globe temperature (WBGT), adjusting for installation-level effects and long-term trends in the negative binomial regression models using block-bootstrap resampling. Ambulatory (out-patient) and reportable event HSI outcomes displayed predominately positive association patterns with the assessed annual indices of heat, whereas hospitalization associations were mostly null. For example, a one-degree Fahrenheit (°F) (or 0.55°C) increase in mean temperature between May and September was associated with a 1.16 (95% confidence interval [CI]: 1.11, 1.29) times greater rate of ambulatory encounters. The annual-scaled rate ratios and their uncertainties may be applied to climate projections for a wide range of thermal indices to estimate future military and civilian HSI burdens and impacts to medical resources.
Topics: Humans; Military Personnel; Heat Stress Disorders; Temperature; Climate; Heat-Shock Response
PubMed: 36417342
DOI: 10.1371/journal.pone.0263803 -
Cureus Sep 2022Although rare in the U.S invasive Fusariosis (IF) is increasingly being recognized as a cause of severe invasive fungal disease in patients with neutropenia in the...
Although rare in the U.S invasive Fusariosis (IF) is increasingly being recognized as a cause of severe invasive fungal disease in patients with neutropenia in the setting of hematologic malignancy and hematopoietic stem cell transplants (HSCT). IF in these patients is associated with high mortality, moreover there are no guidelines on effective therapy, thus early diagnosis and involvement of an expert with experience in treating Fusariosis are imperative. We present a case of IF in a patient with profound prolonged neutropenia in the setting of chemotherapy for relapsed, refractory acute myeloid leukemia. A 33-year-old woman with relapsed acute myeloid leukemia (AML) was hospitalized for re-induction chemotherapy. Five days post cycle 1 she became neutropenic. She was treated with prophylactic antimicrobials that included acyclovir, levofloxacin, and Posaconazole. On day sixty she began to run a high-grade fever. The physical exam was remarkable for a temperature of 102 degrees Fahrenheit and a heart rate of 116 beats per minute. Complete blood count was remarkable for 130 WBC/ml, Hb 6.5 g/dl, hematocrit (HCT) 18.7%, 13000 platelets/ml, absolute neutrophils counts (ANC) of 0. Her CT chest showed new bilateral lung nodules. Antibiotics were changed to cefepime, vancomycin, and metronidazole on day sixty-two without response. On day sixty-five meropenem was started and cefepime stopped. On day sixty-eight posaconazole was stopped and amphotericin B was started and two days later fever became low grade. She developed hyperpigmented skin lesions with necrotic centers on extremities that were biopsied. Histopathology staining favored the presence of rare fungal hyphae. The culture of the biopsy sample grew that was identified by DNA sequencing as . Voriconazole and terbinafine were added. Her fevers resolved within the next 24 hours and she remained afebrile. is a hyaline mold present in the environment. Infection is acquired by inoculation into the skin, intravascular devices, or inhalation. IF incidence is low in the United States. and are the most predominant disease-causing species complexes. Invasive Fusariosis (IF) is a rare disease seen in patients with hematologic malignancy and hematopoietic stem cell transplants (HSCT) with profound neutropenia. Immunocompromised patients suffer disseminated disease to multiple sites as in this case, with mortality rates of between sixty to eighty percent in this patient population. Blood and skin lesions biopsy cultures are diagnostic. Blood cultures are positive in up to sixty percent of cases in about four days. Polymerase chain reaction (PCR) can identify but species identification by PCR is difficult. Newer molecular methods are better for species identification. Histopathology can be helpful. Differential diagnoses include invasive aspergillosis (IA), mucormycosis, mycobacterial and dimorphic fungal infections. There are no guidelines for standard therapy. Amphotericin B or voriconazole are preferred. Combination therapy may be indicated. Neutrophil recovery is crucial. Adjunctive and preventive measures have roles.
PubMed: 36277532
DOI: 10.7759/cureus.29303 -
Case Reports in Critical Care 2022Methylenedioxymethamphetamine (MDMA) is a psychoactive substance that is used commonly as a recreational drug at rave music festivals. MDMA intoxication can cause a...
Methylenedioxymethamphetamine (MDMA) is a psychoactive substance that is used commonly as a recreational drug at rave music festivals. MDMA intoxication can cause a myriad of symptoms and side effects including the manifestation of hyperpyrexia in patients. Hyperpyrexia can mimic a heat stroke and ultimately lead to various forms of end-organ damage. The most common methods used in treating MDMA-induced hyperpyrexia focus on the rapid reduction of core body temperature. Various off-label medications have also been used in combating MDMA-induced hyperpyrexia. Dantrolene is one such medication, although its role in the treatment of MDMA intoxication remains uncertain. This case series preliminarily examines the efficacy of dantrolene in mitigating MDMA-induced hyperpyrexia and potentially reducing the risk of end-organ damage in patients suffering from MDMA overdose. This study focuses on nine patients who presented after ingesting various forms of MDMA at "rave" music events. All patients were found to be hyperthermic in the field with a maximum core body temperature of 109 degrees Fahrenheit. All patients were immediately managed by cooling measures, and seven patients additionally received dantrolene in the field before being transferred to Arrowhead Regional Medical Center. Upon arrival to the hospital, nearly every patient was found to have significantly decreased body temperatures when compared to previously measured body temperatures out in the field. However, nearly all patients in the study were also noted to have laboratory abnormalities consistent with various forms of end-organ damage. The degree and severity of end-organ damage observed in MDMA-induced hyperpyrexia seem to be a function of initial core body temperature. Higher core body temperature tends to correlate with more forms of end-organ damage and a higher severity of end-organ damage. Intervention with dantrolene and cooling measures appeared to have no effect on reducing the risk of developing end-organ damage in this patient population.
PubMed: 36065452
DOI: 10.1155/2022/5346792 -
Environmental Monitoring and Assessment Jun 2022The new summer index (SSI) which was established to determine climate comfort was classified according to the index. Climatic comfort areas will increase and thus...
The new summer index (SSI) which was established to determine climate comfort was classified according to the index. Climatic comfort areas will increase and thus raising the quality of living in areas. The temperature values felt in the study were calculated with the SSI formula, and then the maps of the study area were classified. The study area was the Hayal Park and its surroundings in the Toros Quarter of Cukurova District, which is surrounded by multi-story and dense buildings in the north of Adana. Although the vertical construction is very high, it is richer in terms of green areas compared to other large central districts. Cukurova, which is one of the largest districts of Adana (according to population), has Seyhan dam lake in the north and Seyhan district in the south. The study area is on the border of Seyhan district and is adjacent to Yüreğir and Sarıçam districts. With the portable Smart SENSOR AS 847 measuring device, temperature and relative humidity were measured at 1.5 m above the ground on Tuesday, August 20 at 07.00, at 14.00, and 21.00. Bioclimatic comfort areas were determined by measuring temperature and relative humidity at 25 points with different textures in the study area. In this study, measured instantaneous temperature (°C) and relative humidity (%) data were transferred to GIS medium by ArcGIS 10.6 program and then modeled with the Kriging method, which is one of the interpolation methods, and temperature and relative humidity maps were created. The temperature map created in degrees Celsius (°C) by the Kriging method and was converted to Fahrenheit degrees (°F) in the Raster Calculator. The reason for this change is that SSI is calculated with the formula Fahrenheit (°F). These maps were then calculated on the Raster Calculator using the SSI formula, and sensed temperature values were obtained The SSI, which normally has 8 classes, has 3 classes in the study area. These classes are 83 ≤ SSI < 91 slightly hot, 91 ≤ SSI < 100 hot, and 100 ≤ SSI < 112 very hot. When we look at the maps, the places outside of Hayal Park are in the hot class at 07.00 in the morning, and we can see that the green spaces have a positive effect on the bioclimatic comfort areas. The small area is in a very hot class. When we look at 14.00 h, it is a totally hot class. Normally, the temperature is the highest of these times and also coincides with the multi-story buildings in the study area; asphalt and concrete areas increased the temperature. As a result, there is a very hot air in the study area. It was determined that the maps identified non-comfortable areas. Since urban form and settlement affect climate comfort values, the urban plan should be revised, and the area should be brought to the bioclimatic comfort value range. For reducing the effect of temperature in the working area and creating comfortable areas is increasing the density of green areas compared to asphalt and concrete areas. Considering that the Cukurova district will grow further, urban planning should be done very well to reach the comfort range in the following settlements.
Topics: Cities; City Planning; Data Collection; Environmental Monitoring; Hot Temperature; Parks, Recreational; Temperature
PubMed: 35731448
DOI: 10.1007/s10661-022-10172-y -
Journal of Theoretical Biology Jul 2022The many respiratory viruses that cause influenza-like illness (ILI) are reported and tracked as one entity, defined by the CDC as a group of symptoms that include a...
The many respiratory viruses that cause influenza-like illness (ILI) are reported and tracked as one entity, defined by the CDC as a group of symptoms that include a fever of 100 degrees Fahrenheit, a cough, and/or a sore throat. In the United States alone, ILI impacts 9-49 million people every year. While tracking ILI as a single clinical syndrome is informative in many respects, the underlying viruses differ in parameters and outbreak properties. Most existing models treat either a single respiratory virus or ILI as a whole. However, there is a need for models capable of comparing several individual viruses that cause respiratory illness, including ILI. To address this need, here we present a flexible model and simulations of epidemics for influenza, RSV, rhinovirus, seasonal coronavirus, adenovirus, and SARS/MERS, parameterized by a systematic literature review and accompanied by a global sensitivity analysis. We find that for these biological causes of ILI, their parameter values, timing, prevalence, and proportional contributions differ substantially. These results demonstrate that distinguishing the viruses that cause ILI will be an important aspect of future work on diagnostics, mitigation, modeling, and preparation for future pandemics.
Topics: Epidemics; Humans; Influenza, Human; Rhinovirus; Virus Diseases; Viruses
PubMed: 35490763
DOI: 10.1016/j.jtbi.2022.111145 -
Journal of Nepal Health Research Council Dec 2021Body Temperature is one of the most common and an important sign of health and disease. Considering the need of keeping physical distance, newer methods have evolved...
BACKGROUND
Body Temperature is one of the most common and an important sign of health and disease. Considering the need of keeping physical distance, newer methods have evolved such as; thermal imaging systems which have been used by several countries during epidemics. Therefore, the present study was conducted to compare body temperatures obtained with thermo graphic camera and commercially available thermal gun with reference to standard digital clinical thermometer.
METHODS
The study was comparative analytical in nature and quantitative method was used to collect data. Temperatures in degrees Fahrenheit were taken simultaneously using the three different thermometers in 101 patients at the outpatient fever screening clinic at Tribhuvan University Teaching Hospital, Kathmandu. The Bland Altman statistical test was used to assess the concordance by the 95% limits of agreement.
RESULTS
The thermo-graphic camera gave concordance (limits of agreement-0.0360 to 0.0440 °F) with standard digital clinical thermometer. Similarly, commercially available thermal gun gave the concordance (limits of agreement 0.0042 to 0.1293 °F) with standard digital clinical thermometer.
CONCLUSIONS
The results of the present study show that both thermo-graphic camera and thermal gun were found to be concordant compared to digital clinical thermometer. Therefore, it could be a preferable option for the screening of fever in mass number of individuals as part of an initial check at entry points.
Topics: Fever; Humans; Nepal; Temperature; Tertiary Care Centers; Thermometers
PubMed: 35140439
DOI: 10.33314/jnhrc.v19i3.3511