Physical Partitions Research Articles

Performance modeling and running strategy of parallel cdugksFOAM program

The cdugksFOAM program realizes the physical space grid and the velocity space grid in parallel at the same time. Its distinguishing feature lies in its potential for large-scale parallelism. However, the running time of the cdugksFOAM program is significantly dependent on the number of physical and velocity space partitions. In order to find the optimal partitioning strategies for a specific CFD problem running on a parallel computer, we performed performance modeling of the cdugksFOAM program. Firstly, we proposed a floating-point operations model, a MPI communication volume model, and a memory consumption model. Based on these models, we established a Roofline model to predict the computational time, and a model to predict communication time. According to the computational time model and the communication time model, the execution time model was proposed and its effectiveness was verified with two cases. Finally, the optimal running strategy that minimizes the product of the number of computing nodes and execution time was identified, providing meaningful guidance for the economic execution of the program.

Entanglement island versus massless gravity

Entanglement islands play an essential role in the recent breakthrough in addressing the black hole information paradox. Inspired by double holography, it is conjectured that the entanglement islands can exist only in massive gravity. There are many pieces of evidence but also debates for this conjecture. This paper recovers the massless entanglement island in wedge holography with negative DGP gravity on the brane. However, the spectrum of negative DGP gravity includes a massive ghost, implying the model is unstable. Our work supports the view that there is no entanglement island in a well-defined braneworld model of massless gravity if one divides the radiation and black hole regions by minimizing entanglement entropy. However, such a partition results in a zero radiation region containing no information. Whether there are other physical non-trivial partitions of the radiation region is an open question and deserves further study.

XGNN: Boosting Multi-GPU GNN Training via Global GNN Memory Store

GPUs are commonly utilized to accelerate GNN training, particularly on a multi-GPU server with high-speed interconnects (e.g., NVLink and NVSwitch). However, the rapidly increasing scale of graphs poses a challenge to applying GNN to real-world applications, due to limited GPU memory. This paper presents XGNN, a multi-GPU GNN training system that fully utilizes system memory (e.g., GPU and host memory), as well as high-speed interconnects. The core design of XGNN is the Global GNN Memory Store (GGMS), which abstracts underlying resources to provide a unified memory store for GNN training. It partitions hybrid input data, including graph topological and feature data, across both GPU and host memory. GGMS also provides easy-to-use APIs for GNN applications to access data transparently, forwarding data access requests to the actual physical data partitions automatically. Evaluation on various multi-GPU platforms using three common GNN models with four large-scale datasets shows that XGNN outperforms DGL, Quiver and DGL+C by up to 7.9X (from 2.3X), 15.7X (from 3.3X) and 2.8X (from 1.3X), respectively.

Preparing for the next pandemic: Minimizing airborne transmission in general inpatient wards through management practices

Existing infection control studies in hospitals focused on rooms with special ventilation requirements. Study on proper management practices and ventilation strategies in general inpatient wards are critical but currently lacking. To identify the simple operational practices that can limit airborne transmission within a general inpatient ward with the patient cubicle, nursing station and corridor, this study investigates the effects of infected patient locations, air change rates (ACH) and door opening angles on bioaerosol dispersion using a novel tracer gas sensor network. Experimental results show that the supply inlet and infected patient locations significantly affects the distribution and dispersion of the tracer gas within the ward. Using a higher ventilation rate to achieve a lower average airborne pathogen concentration can cause more mixing of air and a wider dispersion of airborne pathogens. Localization of bioaerosols near the source through ventilation controls, a low ACH and proper patient location near the exhaust can minimize the air turbulence and the spread and reduce the infection risks of the susceptibles. Using physical partitions or objects as shields against airborne contaminants can unpredictably influence the airflow patterns, airflow evaluations should hence be done on a case-by-case basis. The methodology established in this study puts forward an economical and fast way for evaluating airborne infection risk, and the experimental results can be useful references for building engineers and hospital facility managers to formulate proper strategies for risk assessment and infection control.

Abstract 6162: High resolution detection of HER2 copy number variation in admixed breast cancer cell lines and HER2+ FFPE donor tissue using a digital PCR multigene reference panel

Abstract The measurement of HER2 (ERBB2) gene amplification guides both the prognosis and treatment of breast cancer, as amplification correlates with worse outcomes and the recommendation for anti-HER2 treatment. Digital PCR (dPCR) can serve as a useful tool for the direct quantification of copy number variants (CNV) in this gene, without the need for calibration standards as required for qPCR, or labor-intensive histological techniques such as FISH. Furthermore, increasing the number of available partitions in a digital PCR reaction can yield substantial gains in precision, thus offering the potential for ultra-high resolution discrimination of copy number changes. In this study, we evaluated the utility of a multiplex dPCR assay for the high-resolution detection of HER2 copy number variation in clinically relevant samples. The precision achievable by digital PCR correlates with the number of partitions, and the resolution of small CNV differences greatly relies on high precision. We utilized a dPCR setup with ~100,000 physical partitions per reaction, which allowed for a theoretical precision (relative confidence) of 1%, assuming optimal input and template. Five single-plex primer and probe sets, published by the National Institute of Standards and Technology, were assembled and optimized into a multiplex configuration. The final 5-plex consisted of four reference genes and HER2 as the target of interest. The accuracy and precision of the optimized five-plex assay was tested in nine breast cancer cell lines with established HER2 amplification ratios, ranging from 1.3 to 70 fold. The assay demonstrated the precise and accurate measurement of the HER2 amplification ratio across all nine cell lines over a wide dynamic range of sample input. Along with increasing the reaction partition number, the use of multiple reference genes also improved the precision of the HER2 amplification ratio measurement and avoided inaccurate copy number calls due to outlier references. The resolution of the assay was evaluated using admixed samples simulating low tumor fraction. A minimum of a 1.03 fold difference (3% difference from wild type) was detected with statistical significance. Assay concordance was evaluated against IHC-characterized HER2+ FFPE donor tissue with concordant FISH/CISH results. The assay demonstrated robust performance in clinically relevant sample types, supporting further investigation of dPCR as a complementary or even alternative diagnostic approach to current methods. Citation Format: Tyler Landrith, Samantha Smith, Jennifer Chan, Mari Christensen, Yu Chuan Tai, Megan Gonzales, William Yee, Nicolas Newton, Wouter Pattje, Patrick Bogard, Wei Yang. High resolution detection of HER2 copy number variation in admixed breast cancer cell lines and HER2+ FFPE donor tissue using a digital PCR multigene reference panel [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 6162.

Healthcare providers perceptions regarding the presence of Birth Companion during childbirth at a tertiary care hospital in India

BackgroundDespite an increase in institutional births and a fall in maternal mortality, the satisfaction of women with their birthing experience in public health institutions is low. Birth Companion (BC) is an important part of the Labour Room Quality Improvement Initiative introduced by the Government of India in 2017. Despite mandates, its implementation has been unsatisfactory. Little is known about the perception of healthcare providers about BC.MethodsWe conducted a facility-based, cross-sectional quantitative study with doctors and nurses in a tertiary care hospital in Delhi, India to gauge their awareness, perception and knowledge about BC. Following universal total population sampling, the participants were administered a questionnaire, which was completed by 96 of 115 serving doctors (response rate of 83%), and 55 of 105 serving nurses (response rate of 52%).ResultsMost (93%) healthcare providers were aware of the concept of BC, WHO’s recommendation (83%) and Government’s instructions (68%) on BC during labour. A woman’s mother was the BC of choice (70%) closely followed by her husband (69%). Ninety-five percent of providers agreed that the presence of a BC during labour will be beneficial, in providing emotional support, boosting the woman’s confidence, providing comfort measures, helping in the early initiation of breastfeeding, reducing post-partum depression, humanizing labour, reducing the need for analgesia and increasing chances of spontaneous vaginal births. Yet, support for the introduction of BC in their hospital was low due to institutional barriers like overcrowding, lack of privacy, hospital policy, risk of infection; privacy issues and costs.ConclusionsWidespread adoption of the concept of BC would require, besides directives, a buy-in by the providers, and action on their suggestions. These include greater funding for hospitals, creating physical partitions to ensure privacy, sensitization and training of health providers and BC, incentivizing hospitals and birthing women, formulation of guidelines on BC, standards setting and a change in institutional culture.

Monkeypox virus contamination in an office-based workplace environment

Monkeypox virus contamination in an office-based workplace environment

Exposure Risk to Medical Staff in a Nasopharyngeal Swab Sampling Cabin under Four Different Ventilation Strategies

Medical staff working in a nasopharyngeal swab sampling cabin are exposed to a higher exposure risk of COVID-19. In this study, computational fluid dynamics (CFD) are used to evaluate the exposure risk to medical staff in a nasopharyngeal swab sampling cabin of Chinese customs under four different ventilation strategies, i.e., multiple supply fans ventilation (MSFV), multiple exhaust fans ventilation (MEFV), single exhaust fan and outer windows closed ventilation (SEFV), and single exhaust fan and outer windows opened ventilation (SEFV-W). The impact of physical partitions on exposure risk is also discussed. The results show that MSFV performed best in reducing exposure risk. No significant difference was found between MEFV and SEFV. SEFV-W performed better than SEFV with a ventilation rate of 10–50 L/(s∙Person), while it performed worse with a ventilation rate of 50–90 L/(s∙Person). The exposure risk to medical staff did not decrease linearly with the increase in the ventilation flow rate under the four ventilation strategies. For MSFV, the installation of partitions is conducive to the reduction in the exposure risk. This study is expected to provide some guidance for ventilation designs in sampling cabins.

A new possible route of airborne transmission caused by the use of a physical partition

This study experimentally examines the effect of a physical partition on the risk of short-distance cross-infection in a densely occupied canteen. A human subject was employed to simulate an infected person and three thermal manikins were used to simulate the exposed persons, who sat around the same dining table. Four influential factors were examined, including the height and the type of physical partition (i.e., cross-partition and linear-partition), and the head posture and the activity (i.e., dining or not) of the infected person. The CO2 exhaled by the subject was used to simulate the exhaled air. The ratio of the CO2 concentration at the monitoring points to the background CO2 concentration in the canteen was defined as the exposure index. A partition that is not lower than the breathing level of the infected person by 3–5 cm can effectively block the horizontal development of the expiratory jet. Compared with no partition, the use of cross-partition and linear-partition results in an increase of the exposure index in the source compartment (i.e., the area facing the subject) by 97.2% and 25.5%, respectively. It takes, on average, 11 min for the CO2 concentration in the source compartment to decay back to the background concentration, after the subject completes dining and leaves the seat. This implies that a latter diner is possibly exposed to the high concentration of the expiratory air released by the former diner, presenting a new possible transmission route. The findings obtained in this study should contribute to an improved design and application of physical partitions.

Establishment of scalable nanoliter digital LAMP technology for the quantitative detection of multiple myeloproliferative neoplasm molecular markers

Myeloproliferative neoplasms (MPNs) are a type of chronic hematological tumor accompanied by bone marrow failure or leukemia. A nanoparticle-assisted digital loop-mediated isothermal amplification (nano-dLAMP) platform was established for the analysis of MPNs in this study. Microarray chips with four physical partitions were fabricated for the simultaneous detection of calreticulin type 1 (CALR-1), calreticulin type 2 (CALR-2), and janus kinase 2 V617F (JAK2 V617F) mutations and an internal reference gene. Polymerase chain reaction (PCR) additives and nanoparticles were used to make the traditional loop mediated isothermal amplification (LAMP) suitable for nanoliter-scale amplification. The results suggested that nanoparticles could improve the amplification performance of nanoliter LAMP. Quantitative detection of the main MPN molecular markers could be performed simultaneously in one four-partition microarray chip within 1 h. The detection sensitivity values for CALR-1, CALR-2, and JAK2 V617F were 0.5 %, 0.1 %, and 0.5 % mutation burden, respectively. The agreement between the developed platform and the commercial Quantstudio 3D was high at 99 % (280/281). This accurate, rapid, multiplex, and inexpensive nano-dLAMP platform could be a promising tool for clinical diagnosis in the future.

28.1: Invited Paper: Two‐dimensional local dimming by using multiple physical partitions of grooved and edge‐lit light guide plate

28.1: <i>Invited Paper:</i> Two‐dimensional local dimming by using multiple physical partitions of grooved and edge‐lit light guide plate

User Placement and Optimal Cooling Energy for Co-working Building Spaces

Increasing real estate and other infrastructure costs have resulted in the trend of co-working offices where users pay as they use for individual desks. Co-working offices that provide personalized comfort need to address users with potentially widely varying thermal comfort preferences. Providing personalized comfort in cabins separated by physical partitions with neighboring thermal zones or open-plan offices with a single actuator has received attention in the literature. In this article, the problem of minimizing user discomfort in open-plan co-working offices with multiple actuators while being cognizant of the energy consumed is considered. Specifically, the decision problems of assigning users to desks based on their thermal preferences and jointly controlling the multiple actuators are addressed. The non-linearities in the underlying thermodynamic constraints and the seating decision together make the problem computationally hard. A two-step heuristic that addresses these issues is presented. First, using a model that accounts for spatio-temporal thermodynamics, a one-time assignment of users to desks is performed that reduces the thermal resistance faced by the HVAC systems to provide the preferred comfort levels. Next, the setpoints are decided for all actuators to jointly minimize user discomfort by optimization and model-predictive control. Further, scalability is addressed by clustering user preferences and the associated HVAC actuators’ setpoints for the cases where a large number of actuators may be present in the room.

Hadal zones of the Northwest Pacific Ocean

Understanding the extent of the hadal ecosystem (habitats exceeding 6000 m water depth) is convoluted due to the complexity of seafloor geomorphology that accounts for 45% of the total ocean depth range. Furthermore, at such great depths, features such as fracture zones and basins, although numerous, are less prominent and therefore have drawn less focus compared to the conspicuous subduction trenches that are typically associated with hadal science. Here we focus on the Northwest Pacific Ocean, where the majority of hadal features are located, to evaluate the true extent of the deepest marine ecosystem. This analysis has highlighted that the Mariana Trench, in terms of continuous hadal habitat, is in fact five isolated areas, with the most northern being what Russian scientists used to call the Volcano Trench. Conversely, we identified that there are no physical partitions either north or south of the Japan Trench to isolate it from the neighbouring Kuril-Kamchatka or Izu-Bonin trenches respectively, thus it forms one continuous hadal habitat. By evaluating the frequency and distribution of smaller features, such as basins and fracture zones, we conclude that in the northwest Pacific, the total area occupied by depths > 6000 m is 2,793,011 km2, which is considerably larger than the 686,114 km2 accounted for by subduction trenches alone. These results demonstrate not only that the hadal ecosystem may be far larger than previously anticipated but that the geomorphology is crucial in understanding the distribution and genetic connectivity of endemic hadal species that inhabit these great depths.

Root and shoot competition lead to contrasting competitive outcomes under water stress: Asystematic review and meta-analysis.

BackgroundCompetition is a critical process that shapes plant communities and interacts with environmental constraints. There are surprising knowledge gaps related to mechanisms that belie competitive processes, though important to natural communities and agricultural systems: the contribution of different plant parts on competitive outcomes and the effect of environmental constraints on these outcomes.ObjectiveStudies that partition competition into root-only and shoot-only interactions assess whether plant parts impose different competitive intensities using physical partitions and serve as an important way to fill knowledge gaps. Given predicted drought escalation due to climate change, we focused a systematic review–including a meta-analysis on the effects of water supply and competitive outcomes.MethodsWe searched ISI Web of Science for peer-reviewed studies and found 2042 results. From which eleven suitable studies, five of which had extractable information of 80 effect sizes on 10 species to test these effects. We used a meta-analysis to compare the log response ratios (lnRR) on biomass for responses to competition between roots, shoots, and full plants at two water levels.ResultsWater availability treatment and competition treatment (root-only, shoot-only, and full plant competition) significantly interacted to affect plant growth responses (p < 0.0001). Root-only and full plant competition are more intense in low water availability (-1.2 and -0.9 mean lnRR, respectively) conditions than shoot-only competition (-0.2 mean lnRR). However, shoot-only competition in high water availability was the most intense (— 0.78 mean lnRR) compared to root-only and full competition (-0.5 and 0.61 mean lnRR, respectively) showing the opposite pattern to low water availability. These results also show that the intensity of full competition is similar to root-only competition and that low water availability intensifies root competition while weakening shoot competition.ConclusionsThe outcome that competition is most intense between roots at low water availability emphasizes the importance of root competition and these patterns of competition may shift in a changing climate, creating further urgency for further studies to fil knowledge gaps addressing issues of drought on plant interactions and communities.

Cloud forecasting: Legal visibility issues in saturated environments

The advent of cloud computing has brought the computing power of corporate data processing and storage centers to lightweight devices. Software-as-a-service cloud subscribers enjoy the convenience of personal devices along with the power and capability of a service. Using logical as opposed to physical partitions across cloud servers, providers supply flexible and scalable resources. Furthermore, the possibility for multitenant accounts promises considerable freedom when establishing access controls for cloud content. For forensic analysts conducting data acquisition, cloud resources present unique challenges. Inherent properties such as dynamic content, multiple sources, and nonlocal content make it difficult for a standard to be developed for evidence gathering in satisfaction of United States federal evidentiary standards in criminal litigation. Development of such standards, while essential for reliable production of evidence at trial, may not be entirely possible given the guarantees to privacy granted by the Fourth Amendment and the Electronic Communications Privacy Act. Privacy of information on a cloud is complicated because the data is stored on resources owned by a third-party provider, accessible by users of an account group, and monitored according to a service level agreement. This research constructs a balancing test for competing considerations of a forensic investigator acquiring information from a cloud.

Plant array chip for the germination and growth screening of Arabidopsis thaliana.

A screening process for the germination and growth of seed is generally required for plant research. Such a repetitive screening process is costly and time-consuming, and its bulky setup requires a lot of space. In particular, the control of the variables, such as light, nutrients, hormones and temperature, is difficult due to the limited space for incubation. In addition, small seeds such as Arabidopsis thaliana are difficult to handle as they are hundreds of microns in diameter and require a more precisely controllable screening environment. However, conventional screening methods involve the seeding of multiple seeds on a single agarose plate without physical partitions. Such methods need to be improved because they lack control over the growth environment and the results are highly dependent on the researchers. To overcome the above-mentioned limitations, a novel seeding array chip has been developed which can be filled with conventional solid agarose while enabling more efficient screening. Individual seeds can be partitioned from each other and a number of different agarose conditions can be tested in a single plant array chip. As a demonstration, we tested the effect of various concentrations of Murashige and Skoog medium and a plant hormone (e.g., abscisic acid) on the growth of Arabidopsis. The chip can efficiently save the space required for screening by providing different conditions for ∼400 seeds in a 59 × 55 mm chip, and it also provides easy observation and analysis of seed growth. The proposed plant array chip is expected to contribute to more efficient screening of essential phenotypes such as germination and growth for both academic and industrial purposes.

Measurement of ventilation and airborne infection risk in large naturally ventilated hospital wards

Airborne pathogens pose a significant threat to human health and this is especially the case in hospital environments which house patients with weakened immune systems. Good ventilation design can reduce risk, however quantifying ventilation performance and its influence on infection risk is difficult, particularly for large naturally ventilated environments with multiple openings. This study applies a pulse-injection gas tracer method to assess potential infection risk and local ventilation rates in a naturally-ventilated environment. Experiments conducted in a 200 m3 cross-ventilated Nightingale ward show that local external wind speeds in the range 1–4 m/s lead to indoor ventilation rates of between 3.4 and 6.5 air changes per hour (ACH). Natural ventilation is shown to be effective in open wards with an even distribution of potential airborne infection risk throughout patient locations. Comparison with a partitioned ward highlighted the potential for protecting neighbouring patients with physical partitions between beds, however, higher tracer concentrations are present in both the vicinity and downstream of the source. Closing the windows to represent winter conditions dramatically increases infection risk, with relative exposure to the tracer increased fourfold compared to the scenarios with the windows open. Extract fans are shown to alleviate this problem suggesting that a hybrid approach utilising the respective strengths of natural and mechanical ventilation may offer the best year-round solution in this and similar settings.

The impact of housing environment attributes on children's academic performance at school: an empirical study of Hong Kong

PurposeThis paper aims to examine the influence of physical housing environments on the learning potential of children. The authors argue for housing design which is attentive to the need for open but personal space with “sufficient physical partitions”.Design/methodology/approachThe research draws on an empirical study of students in two randomly selected Hong Kong secondary schools. The approach includes the use of multiple regression analysis to test the correlation between academic performance and a set of environmental attributes.FindingsHousing design, aspect and size of housing are significant. Academic performance is not dependent on tenure type and this is partly related to mixed tenure, close proximity of differing socio‐economic neighborhoods and the sharing of social capital to provide equal opportunity. However, densely developed high housing is not desirable for children's academic development.Research limitations/implicationsThe location of Hong Kong provides a very specific combination of small land mass, a history of high rise living and a social housing sector and the need to optimize physical space for social ends. Home ownership does not play a role of a stabilizer for children, as observed in other places.Practical implicationsThis paper prompts a reassessment, by housing providers and commissioners, of the link between housing types and long term educational opportunities and the need to devise appropriate partnerships to ensure that housing adds to academic performance rather than undermine it.Social implicationsThe study of the effects of high rise high density housing on children's learning is underdeveloped and should be reassessed in markets, such as that in the UK, where use of the private rented sector is increasingly used to house families who may in the past have been housed directly by the State.Originality/valueThis research attempts to apply quantitative techniques to provide evidence to policy makers that can be replicated in other housing contexts.

Effect of Physical Inactivity on the Oxidation of Saturated and Monounsaturated Dietary Fatty Acids: Results of a Randomized Trial

Objectives:Changes in the way dietary fat is metabolized can be considered causative in obesity. The role of sedentary behavior in this defect has not been determined. We hypothesized that physical inactivity partitions dietary fats toward storage and that a resistance exercise training program mitigates storage.Design:We used bed rest, with randomization to resistance training, as a model of physical inactivity.Setting:The trial took place at the Space Clinic (Toulouse, France).Participants:A total of 18 healthy male volunteers, of mean age ± standard deviation 32.6 ± 4.0 y and body mass index 23.6 ± 0.7 kg/m2, were enrolled.Interventions:An initial 15 d of baseline data collection were followed by 3 mo of strict bed-rest alone (control group, n = 9) or with the addition of supine resistance exercise training every 3 d (exercise group, n = 9).Outcome measures:Oxidation of labeled [d31]palmitate (the main saturated fatty acid of human diet) and [1-13C]oleate (the main monounsaturated fatty acid), body composition, net substrate use, and plasma hormones and metabolites were measured.Results:Between-group comparisons showed that exercise training did not affect oxidation of both oleate (mean difference 5.6%; 95% confidence interval [95% CI], −3.3% to 14.5%; p = 0.20) and palmitate (mean difference −0.2%; 95% CI, −4.1% to 3.6%; p = 0.89). Within-group comparisons, however, showed that inactivity changed oxidation of palmitate in the control group by −11.0% (95% CI, −19.0% to −2.9%; p = 0.01) and in the exercise group by −11.3% (95% CI, −18.4% to −4.2%; p = 0.008). In contrast, bed rest did not significantly affect oleate oxidation within groups. In the control group, the mean difference in oleate oxidation was 3.2% (95% CI, −4.2% to 10.5%; p = 0.34) and 6.8% (95% CI, −1.2% to 14.7%; p = 0.08) in the exercise group.Conclusions:Independent of changes in energy balance (intake and/or output), physical inactivity decreased the oxidation of saturated but not monounsaturated dietary fat. The effect is apparently not compensated by resistance exercise training. These results suggest that Mediterranean diets should be recommended in sedentary subjects and recumbent patients.

Divide and conquer [SoC design

The complexity of chip-level integration has held back the effective logic density of SoC designs - making it difficult to build complex chips, such as high-integration set-top box controllers. That could change as teams adopt methods taking advantage of tools that can deal with logical and physical partitions separately. At the physical level, system-on-chip (SoC) design methods have evolved to increase density and shorten implementation time by improving predictability on timing, routing and design integrity closure. Methods based on physical partitions have taken full advantage of emerging tools and available chip density. The effectiveness of the approach comes from three elements that have been made available recently in back-end tools.