gSuite: A Flexible and Framework Independent Benchmark Suite for Graph Neural Network Inference on GPUs

As the interest to Graph Neural Networks (GNNs) is growing, the importance of benchmarking and performance characterization studies of GNNs is increasing. So far, we have seen many studies that investigate and present the performance and computational efficiency of GNNs. However, the work done so far has been carried out using a few high-level GNN frameworks. Although these frameworks provide ease of use, they contain too many dependencies to other existing libraries. The layers of implementation details and the dependencies complicate the performance analysis of GNN models that are built on top of these frameworks, especially while using architectural simulators. Furthermore, different approaches on GNN computation are generally overlooked in prior characterization studies, and merely one of the common computational models is evaluated. Based on these shortcomings and needs that we observed, we developed a benchmark suite that is framework independent, supporting versatile computational models, easily configurable and can be used with architectural simulators without additional effort. Our benchmark suite, which we call gSuite, makes use of only hardware vendor's libraries and therefore it is independent of any other frameworks. gSuite enables performing detailed performance characterization studies on GNN Inference using both contemporary GPU profilers and architectural GPU simulators. To illustrate the benefits of our new benchmark suite, we perform a detailed characterization study with a set of well-known GNN models with various datasets; running gSuite both on a real GPU card and a timing-detailed GPU simulator. We also implicate the effect of computational models on performance. We use several evaluation metrics to rigorously measure the performance of GNN computation.Comment: IEEE International Symposium on Workload Characterization (IISWC) 202

Extraintestinal Manifestations in Helicobacter pylori Infection – Iron Deficiency Anemia and Helicobacter pylori

Iron is an essential element for all living organisms. Iron metabolism is mainly controlled by its absorption. Iron deficiency (ID) is the most common nutritional deficiency, causing important clinical outcomes. One of the most common results of ID is iron deficiency anemia (IDA). The ID results from increased physiological needs, blood losses, inadequate intake, and diminished absorption. Helicobacter pylori (H. pylori) infection is one of the important causes of IDA, especially in undetermined and refractory cases

Haptic negotiation and role exchange for collaboration in virtual environments

We investigate how collaborative guidance can be realized in multi-modal virtual environments for dynamic tasks involving motor control. Haptic guidance in our context can be defined as any form of force/tactile feedback that the computer generates to help a user execute a task in a faster, more accurate, and subjectively more pleasing fashion. In particular, we are interested in determining guidance mechanisms that best facilitate task performance and arouse a natural sense of collaboration. We suggest that a haptic guidance system can be further improved if it is supplemented with a role exchange mechanism, which allows the computer to adjust the forces it applies to the user in response to his/her actions. Recent work on collaboration and role exchange presented new perspectives on defining roles and interaction. However existing approaches mainly focus on relatively basic environments where the state of the system can be defined with a few parameters. We designed and implemented a complex and highly dynamic multimodal game for testing our interaction model. Since the state space of our application is complex, role exchange needs to be implemented carefully. We defined a novel negotiation process, which facilitates dynamic communication between the user and the computer, and realizes the exchange of roles using a three-state finite state machine. Our preliminary results indicate that even though the negotiation and role exchange mechanism we adopted does not improve performance in every evaluation criteria, it introduces a more personal and human-like interaction model

Conveying intentions through haptics in human-computer collaboration

Haptics has been used as a natural way for humans to communicate with computers in collaborative virtual environments. Human-computer collaboration is typically achieved by sharing control of the task between a human and a computer operator. An important research challenge in the field addresses the need to realize intention recognition and response, which involves a decision making process between the partners. In an earlier study, we implemented a dynamic role exchange mechanism, which realizes decision making by means of trading the parties' control levels on the task. This mechanism proved to show promise of a more intuitive and comfortable communication. Here, we extend our earlier work to further investigate the utility of a role exchange mechanism in dynamic collaboration tasks. An experiment with 30 participants was conducted to compare the utility of a role exchange mechanism with that of a shared control scheme where the human and the computer share control equally at all times. A no guidance condition is considered as a base case to present the benefits of these two guidance schemes more clearly. Our experiment show that the role exchange scheme maximizes the efficiency of the user, which is the ratio of the work done by the user within the task to the energy spent by her. Furthermore, we explored the added benefits of explicitly displaying the control state by embedding visual and vibrotactile sensory cues on top of the role exchange scheme. We observed that such cues decrease performance slightly, probably because they introduce an extra cognitive load, yet they improve the users' sense of collaboration and interaction with the computer. These cues also create a stronger sense of trust for the user towards her partner's control over the task

Helicobacter pylori Seropositivity and Stool Antigen in Patients With Hyperemesis Gravidarum

The objective of this paper is to investigate whether Helicobacter pylori is an etiologic factor in hyperemesis gravidarum. Thirty one patients with hyperemesis gravidarum and twenty nine pregnant controls without hyperemesis gravidarum were included in this prospective study. All pregnant women were examined both for Helicobacter pylori serum immunoglobulin G antibodies (HpIgG Ab), showing chronic infection, and Helicobacter pylori stool antigens (HpSA), showing active gastrointestinal colonization. Chi-square and Student t tests were used accordingly for statistical analysis. Helicobacter pylori seropositivity was 67.7% in the patients with hyperemesis gravidarum and 79.3% in the control group (χ(2) = 1.02, P = .31). HpSA was detected in 22.6% of patients with hyperemesis gravidarum, whereas 6.9% of patients in the control group. The difference was not statistically significant (χ(2) = 2.89, P = .08). In this study, no relation was found between Helicobacter pylori and hyperemesis gravidarum. The low social status of women in both groups could be one of the reasons for the high prevalence of Hp infection

Human PMS2 deficiency is associated with impaired immunoglobulin class switch recombination

Immunoglobulin (Ig) class switch recombination (CSR) deficiencies are rare primary immunodeficiencies characterized by the lack of switched isotype (IgG/IgA/IgE) production. In some cases, CSR deficiencies can be associated with abnormal somatic hypermutation. Analysis of CSR deficiencies has helped reveal the key functions of CSR-triggering molecules, i.e., CD40L, CD40, and effector molecules such as activation-induced cytidine deaminase and uracil N-glycosylase. We report a new form of B cell–intrinsic CSR deficiency found in three patients with deleterious, homozygous mutations in the gene encoding the PMS2 component of the mismatch repair machinery. CSR was found partially defective in vivo and markedly impaired in vitro. It is characterized by the defective occurrence of double-strand DNA breaks (DSBs) in switch regions and abnormal formation of switch junctions. This observation strongly suggests a role for PMS2 in CSR-induced DSB generation

The impact of bismuth addition to sequential treatment on Helicobacter pylori eradication: A pilot study

The success of the current anti-Helicobacter pylori (H. pylori) treatment protocols is reported to decrease by years, and research is needed to strengthen the H. pylori eradication treatment. Sequential treatment (ST), one of the treatment modalities for H. pylori eradication, includes amoxicillin 1 gr b.i.d and proton pump inhibitor b.i.d for first 5 days and then includes clarithromycin 500 mg b.i.d, metronidazole 500 mg b.i.d and a proton pump inhibitor b.i.d for remaining 5 days. In this study, we investigated efficacy and tolerability of bismuth addition in to ST. We included patients that underwent upper gastrointestinal endoscopy in which H. pylori infection was diagnosed by histological examination of antral and corporal gastric mucosa biopsy. Participants were randomly administered ST or bismuth containing ST (BST) protocols for the first-line H. pylori eradication therapy. Participants have been tested by urea breath test for eradication success 6 weeks after the completion of treatment. One hundred and fifty patients (93 female, 57 male) were enrolled. There were no significant differences in eradication rates for both intention to treat population (70.2%, 95% confidence interval [CI]: 66.3-74.1% vs. 71.8%, 95% CI: 61.8-81.7%, for ST and BST, respectively, p > 0.05) and per protocol population (74.6%, 95% CI: 63.2-85.8% vs. 73.7%, 95% CI: 63.9-83.5% for ST and BST, respectively, p > 0.05). Despite the undeniable effect of bismuth, there may be several possible reasons of unsatisfactory eradication success. Drug administration time, coadministration of other drugs, possible H. pylori resistance to bismuth may affect the eradication success. The addition of bismuth subcitrate to ST regimen does not provide significant increase in eradication rates

WASP regulates suppressor activity of human and murine CD4+CD25+FOXP3+ natural regulatory T cells

A large proportion of Wiskott-Aldrich syndrome (WAS) patients develop autoimmunity and allergy. CD4+CD25+FOXP3+ natural regulatory T (nTreg) cells play a key role in peripheral tolerance to prevent immune responses to self-antigens and allergens. Therefore, we investigated the effect of WAS protein (WASP) deficiency on the distribution and suppressor function of nTreg cells. In WAS−/− mice, the steady-state distribution and phenotype of nTreg cells in the thymus and spleen were normal. However, WAS−/− nTreg cells engrafted poorly in immunized mice, indicating perturbed homeostasis. Moreover, WAS−/− nTreg cells failed to proliferate and to produce transforming growth factor β upon T cell receptor (TCR)/CD28 triggering. WASP-dependent F-actin polarization to the site of TCR triggering might not be involved in WAS−/− nTreg cell defects because this process was also inefficient in wild-type (WT) nTreg cells. Compared with WT nTreg cells, WAS−/− nTreg cells showed reduced in vitro suppressor activity on both WT and WAS−/− effector T cells. Similarly, peripheral nTreg cells were present at normal levels in WAS patients but failed to suppress proliferation of autologous and allogeneic CD4+ effector T cells in vitro. Thus, WASP appears to play an important role in the activation and suppressor function of nTreg cells, and a dysfunction or incorrect localization of nTreg cells may contribute to the development of autoimmunity in WAS patients

Congenital Agenesis of Right Internal Carotid Artery: A Report of Two Cases

Congenital unilateral agenesis of the internal carotid artery (ICA) is a rare anomaly. Due to proper sufficient collateral circulation via the circle of Willis most cases are asymptomatic, but patients can also present with ischemic or hemorrhagic cerebrovascular insults. The absence of the bony carotid canal is essential to differentiate this anomaly from chronic ICA occlusion. Awareness of this situation by clinicians and radiologists is essential because these patients have an increased incidence of various intracranial pathologies. We report two cases of this rare developmental congenital abnormality occurring in two young patients and describe the presentation, diagnosis, determined developmental causes, imaging findings, and complications