Miracle-dz/UniFAR-FTUs huggingface dataset:
MPU: Memory-centric SIMT Processor via In-DRAM Near-bank Computing

With the growing number of data-intensive workloads, GPU, which is the state-of-the-art single-instruction-multiple-thread (SIMT) processor, is hindered by the memory bandwidth wall. To alleviate this bottleneck, previously proposed 3D-stacking near-bank computing accelerators benefit from abundant bank-internal bandwidth by bringing computations closer to the DRAM banks. However, these accelerators are specialized for certain application domains with simple architecture data paths and customized software mapping schemes. For general-purpose scenarios, lightweight hardware designs for diverse data paths, architectural supports for the SIMT programming model, and end-to-end software optimizations remain challenging. To address these issues, we propose Memory-centric Processing Unit (MPU), the first SIMT processor based on 3D-stacking near-bank computing architecture. First, to realize diverse data paths with small overheads, MPU adopts a hybrid pipeline with the capability of offloading instructions to near-bank compute-logic. Second, we explore two architectural supports for the SIMT programming model, including a near-bank shared memory design and a multiple activated row-buffers enhancement. Third, we present an end-to-end compilation flow for MPU to support CUDA programs. To fully utilize MPU’s hybrid pipeline, we develop a backend optimization for the instruction offloading decision. The evaluation results of MPU demonstrate 3.46× speedup and 2.57× energy reduction compared with an NVIDIA Tesla V100 GPU on a set of representative data-intensive workloads.
Non-classical mechanical behavior of an elastic membrane with an independent Gaussian bending rigidity

The present work considers the mechanical behavior of a non-classical elastic membrane with two independent bending rigidities. Our interest focuses on the case when the ratio of the Gaussian bending rigidity to the common flexural rigidity falls within the non-classical range, which cannot be covered by a classical elastic plate with an admissible positive Poisson ratio. Our results for a rectangular elastic membrane with two opposite free edges show that its deflection under a uniform transverse pressure could be considerably (even more than twice) larger than a classical elastic plate under otherwise identical conditions, while its lowest fundamental frequency and critical buckling force could be considerably (even more than 50%) lower than a classical elastic plate under otherwise identical conditions. These unexpected results suggest that, unlike classical elastic plates whose actual mechanical behavior are often insensitive to the value of the admissible positive Poisson ratio, actual mechanical behavior of a non-classical elastic membrane with two independent bending rigidities could be very sensitive to the exact values of the two independent bending rigidities. Therefore, the exact value of the Gaussian bending rigidity could be crucial for such non-classical elastic membranes. Only knowing the values of the flexural rigidity and Poisson ratio is insufficient for accurate prediction of mechanical modeling of such non-classical elastic membranes with two independent bending rigidities (such as some biomembranes and atom-thick monolayer membranes).
Towards Food Image Retrieval via Generalization-Oriented Sampling and Loss Function Design

Food computing has increasingly received widespread attention in the multimedia field. As a basic task of food computing, food image retrieval has wide applications, that is, food image retrieval can help users to find the desired food from a large number of food images. Besides, the retrieved information can be applied to establish a richer database for the subsequent food content-related recommendation. Food image retrieval aims to achieve better performance on novel categories. Thus, it is worth studying to transfer the embedding ability from the training set to the unseen test set, that is, the generalization of the model. Food is influenced by various factors, such as culture and geography, leading to great differences between domains, such as Asian food and western food. Therefore, it is challenging to study the generalization of the model in food image retrieval. In this article, we improve the classical metric learning framework and propose a generalization-oriented sampling strategy, which boosts the generalization of the model by maximizing the intra-class distance from a proportion of positive pairs to avoid the excessive distance compression in the embedding space. Considering that the existing optimization process is in an opposite direction to our proposed sampling strategy, we further propose an adaptive gradient assignment policy named gradient-adaptive optimization, which can alleviate the intra-class distance compression during optimization by assigning different gradients to different samples. Extensive evaluation on three popular food image datasets demonstrates the effectiveness of the proposed method. We also experiment on three popular general datasets to prove that solving the problem from the generalization can also improve the performance of general image retrieval. Code is available at https://github.com/Jiajun-ISIA/Generalization-oriented-Sampling-and-Loss.
Online Schedule Randomization to Mitigate Timing Attacks in 5G Periodic URLLC Communications

Ultra-reliable low-latency communication (URLLC) in 5G networks is designed to support time-critical applications such as industrial control systems (ICSs), where user equipment (UEs) communicate with a base station (BS) with very high reliability and low latency. Most of these communications in ICSs are periodic and associated with hard deadlines. To provide a reliable service while satisfying the hard deadlines, the BS usually reserves slots and frequencies and precomputes the schedule for such UEs. The same schedule repeats over time, which makes the slots and frequencies predictable. However, an attacker can exploit this aspect and launch timing attacks disrupting specific communication, thereby, undermining the safety of the system. To mitigate such attacks, we present an online strategy that randomizes the scheduled slots and frequencies over time without violating the flow deadlines. We use Kullback-Leibler divergence to measure the randomness in the schedules generated by our strategy with reference to a hypothetical truly random strategy. We perform security analysis of our proposed strategy using Prediction Probability to measure the predictability in the slots of the generated schedules. We evaluate the performance of our strategy against a state-of-the-art baseline, and show that our strategy performs better than the baseline across all parameter settings.
CDX2-positive Cancer of Unknown Primary With Upper-body Paralysis Was Dramatically Improved by Colorectal Cancer Chemotherapy

Background: Caudal-related homeobox transcription factor 2 (CDX2) is expressed in intestinal epithelial cells. CDX2 is a very sensitive marker for the identification of small and large intestine tumors, which is expressed in 85.7-100% of colorectal cancer (CRC) cases. Case Report: A 61-year-old female had been suffering from left shoulder pain for one month. Computed tomography showed osteolytic masses extending to the vertebral arch in the C5, C6, C7, and Th3 vertebral bodies. In addition, a thickening of the sigmoid colon was observed from the rectal-sigmoid colon, suggesting CRC. A colon biopsy revealed poorly differentiated adenocarcinoma and the vertebra excision was metastatic adenocarcinoma. However, immunohistochemically, the vertebra tumor was negative for CK7 and CK20 but positive for CDX2. Therefore, we made the diagnosis of CRC with bone metastasis and decided to start treatment for CRC. Posterior stabilization was performed for the spinal tumor 6 days after admission. About one month after admission, she started treatment with chemotherapy. Initially, her left hand could not move, and she could barely hold the pen with her right hand. After adding cetuximab for the third time, she became able to bend the dorsiflexion of her right wrist joint, grasp a stick with her right hand, and move the fingertips of her left hand a little. Conclusion: The presented case could not be diagnosed as CRC unless CDX2 was examined. Upper body paralysis due to CRC bone metastasis was improved by chemotherapy.
A genome-wide association study and genomic prediction for Phakopsora pachyrhizi resistance in soybean

Soybean brown rust (SBR), caused by Phakopsora pachyrhizi, is a devastating fungal disease that threatens global soybean production. This study conducted a genome-wide association study (GWAS) with seven models on a panel of 3,082 soybean accessions to identify the markers associated with SBR resistance by 30,314 high quality single nucleotide polymorphism (SNPs). Then five genomic selection (GS) models, including Ridge regression best linear unbiased predictor (rrBLUP), Genomic best linear unbiased predictor (gBLUP), Bayesian least absolute shrinkage and selection operator (Bayesian LASSO), Random Forest (RF), and Support vector machines (SVM), were used to predict breeding values of SBR resistance using whole genome SNP sets and GWAS-based marker sets. Four SNPs, namely Gm18_57,223,391 (LOD = 2.69), Gm16_29,491,946 (LOD = 3.86), Gm06_45,035,185 (LOD = 4.74), and Gm18_51,994,200 (LOD = 3.60), were located near the reported P. pachyrhizi R genes, Rpp1, Rpp2, Rpp3, and Rpp4, respectively. Other significant SNPs, including Gm02_7,235,181 (LOD = 7.91), Gm02_7234594 (LOD = 7.61), Gm03_38,913,029 (LOD = 6.85), Gm04_46,003,059 (LOD = 6.03), Gm09_1,951,644 (LOD = 10.07), Gm10_39,142,024 (LOD = 7.12), Gm12_28,136,735 (LOD = 7.03), Gm13_16,350,701(LOD = 5.63), Gm14_6,185,611 (LOD = 5.51), and Gm19_44,734,953 (LOD = 6.02), were associated with abundant disease resistance genes, such as Glyma.02G084100, Glyma.03G175300, Glyma.04g189500, Glyma.09G023800, Glyma.12G160400, Glyma.13G064500, Glyma.14g073300, and Glyma.19G190200. The annotations of these genes included but not limited to: LRR class gene, cytochrome 450, cell wall structure, RCC1, NAC, ABC transporter, F-box domain, etc. The GWAS based markers showed more accuracies in genomic prediction than the whole genome SNPs, and Bayesian LASSO model was the ideal model in SBR resistance prediction with 44.5% ~ 60.4% accuracies. This study aids breeders in predicting selection accuracy of complex traits such as disease resistance and can shorten the soybean breeding cycle by the identified markers
Short-term use of CGM in youth onset type 2 diabetes is associated with behavioral modifications

Background Continuous glucose monitoring (CGM) is beneficial to glycemic control in youth with type 1 diabetes (T1D) and adults with type 2 diabetes (T2D); however, studies in youth with T2D are limited. Objective Determine if 10-day trial CGM use in youth with T2D improves glycemic control and behavioral modifications. Methods Youth with T2D > 3 months, on insulin, with no prior CGM use were enrolled. Staff placed CGM and provided education. Participants received 5-day and 10-day follow-up phone calls to review CGM data, behavioral modifications, and adjust insulin doses as needed. We compared 5-day to 10-day TIR, and baseline to 3-6 month HbA1c via paired t-test. Results Participants (n=41) had median age of 16.2 y, were 61% female, 81% NH Black, median diabetes duration of 0.8 y, and baseline HbA1c of 10.3%. A majority had household income<$50,000 (81%) and parental education level of HS or less (73%). Average 5-day TIR 49% was similar to 10-day TIR 51% (p=0.62). There was no change in HbA1c after 3-6 months (10.2% v 10.3%, p=0.89). Nineteen participants completed full 10-day CGM use; of those, 84% wanted a CGM long-term. Adolescents reported behavioral changes including increased blood sugar checks, increased insulin administration and overall improved diabetes management. Conclusion Although 10-day CGM use did not impact short-term or long-term glycemic control in youth with T2D, most participants reported behavioral changes and wanted to continue using CGM. Future studies with longer use of CGM may clarify the potential impact of CGM in youth with T2D.
Machine learning analysis of humoral and cellular responses to SARS-CoV-2 infection in young adults

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) induces B and T cell responses, contributing to virus neutralization. In a cohort of 2,911 young adults, we identified 65 individuals who had an asymptomatic or mildly symptomatic SARS-CoV-2 infection and characterized their humoral and T cell responses to the Spike (S), Nucleocapsid (N) and Membrane (M) proteins. We found that previous infection induced CD4 T cells that vigorously responded to pools of peptides derived from the S and N proteins. By using statistical and machine learning models, we observed that the T cell response highly correlated with a compound titer of antibodies against the Receptor Binding Domain (RBD), S and N. However, while serum antibodies decayed over time, the cellular phenotype of these individuals remained stable over four months. Our computational analysis demonstrates that in young adults, asymptomatic and paucisymptomatic SARS-CoV-2 infections can induce robust and long-lasting CD4 T cell responses that exhibit slower decays than antibody titers. These observations imply that next-generation COVID-19 vaccines should be designed to induce stronger cellular responses to sustain the generation of potent neutralizing antibodies.
Incidence and risk factors of acute kidney injury in cancer patients treated with immune checkpoint inhibitors: a systematic review and meta-analysis

Background The incidence and risk factors of acute kidney injury (AKI) in patients with malignancies receiving immune checkpoint inhibitors (ICIs) are being extensively reported with their widespread application. Objective This study aimed to quantify the incidence and identify risk factors of AKI in cancer patients treated with ICIs. Methods We searched the electronic databases of PubMed/Medline, Web of Science, Cochrane and Embase before 1 February 2023 on the incidence and risk factors of AKI in patients receiving ICIs and registered the protocol in PROSPERO (CRD42023391939). A random-effect meta-analysis was performed to quantify the pooled incidence estimate of AKI, identify risk factors with pooled odds ratios (ORs) and 95% confidence intervals (95% CIs) and investigate the median latency period of ICI-AKI in patients treated with ICIs. Assessment of study quality, meta-regression, and sensitivity and publication bias analyses were conducted. Results In total, 27 studies consisting of 24048 participants were included in this systematic review and meta-analysis. The overall pooled incidence of AKI secondary to ICIs was 5.7% (95% CI: 3.7%-8.2%). Significant risk factors were older age (OR: 1.01, 95% CI: 1.00–1.03), preexisting chronic kidney disease (CKD) (OR: 2.90, 95% CI: 1.65–5.11), ipilimumab (OR: 2.66, 95% CI: 1.42–4.98), combination of ICIs (OR: 2.45, 95% CI: 1.40–4.31), extrarenal immune-related adverse events (irAEs) (OR: 2.34, 95% CI: 1.53-3.59), and proton pump inhibitor (PPI) (OR: 2.23, 95% CI: 1.88–2.64), nonsteroidal anti-inflammatory drug (NSAID) (OR: 2.61, 95% CI: 1.90–3.57), fluindione (OR: 6.48, 95% CI: 2.72–15.46), diuretic (OR: 1.78, 95% CI: 1.32–2.40) and angiotensin-converting enzyme inhibitors (ACEIs) or angiotensin-receptor blockers (ARBs) (pooled OR: 1.76, 95% CI: 1.15–2.68) use. Median time from ICIs initiation to AKI was 108.07 days. Sensitivity and publication bias analyses indicated robust results for this study. Conclusion The occurrence of AKI following ICIs was not uncommon, with an incidence of 5.7% and a median time interval of 108.07 days after ICIs initiation. Older age, preexisting chronic kidney disease (CKD), ipilimumab, combined use of ICIs, extrarenal irAEs, and PPI, NSAID, fluindione, diuretics and ACEI/ARB use are risk factors for AKI in patients receiving ICIs. Systematic review registration https://www.crd. york.ac. uk/prospero/, identifier CRD42023391939.
Clinical and genetic characteristics in pancreatic cancer from Chinese patients revealed by whole exome sequencing

Background Pancreatic ductal adenocarcinoma (PDAC) is one of the most fatal malignancies worldwide, mostly as a result of the absence of early detection and specific treatment solutions. Consequently, identifying mutational profiles and molecular biomarkers is essential for increasing the viability of precision therapy for pancreatic cancer. Methods We collected blood and tumor tissue samples from 47 Chinese pancreatic cancer patients and used whole-exome sequencing (WES) to evaluate the genetic landscape. Results Our results showed the most frequently somatic alteration genes were KRAS (74.5%), TP53(51.1%), SMAD4 (17%), ARID1A (12.8%), CDKN2A (12.8%), TENM4 (10.6%), TTN (8.5%), RNF43(8.5%), FLG (8.5%) and GAS6 (6.4%) in Chinese PDAC patients. We also found that three deleterious germline mutations (ATM c.4852C>T/p. R1618*, WRN c.1105C>T/p. R369*, PALB2 c.2760dupA/p. Q921Tfs*7) and two novel fusions (BRCA1-RPRML, MIR943 (intergenic)-FGFR3). When compared to the Cancer Genome Atlas (TCGA) database, there is a greater mutation frequency of TENM4 (10.6% vs. 1.6%, p = 0.01), GAS6(6.4% vs. 0.5%, p = 0.035), MMP17(6.4% vs. 0.5%, p = 0.035), ITM2B (6.4% vs. 0.5%, p = 0.035) and USP7 (6.4% vs. 0.5%, p= 0.035) as well as a reduced mutation frequency of SMAD4 (17.0% vs. 31.5%, p = 0.075) and CDKN2A (12.8% vs. 47.3%, p < 0.001) were observed in the Chinese cohort. Among the 41 individuals examined for programmed cell death ligand 1(PD-L1) expression, 15 (36.6%) had positive PD-L1 expression. The median tumor mutational burden (TMB) was found to be 12muts (range, 0124). The TMB index was higher in patients with mutant-type KRAS MUT/TP53 MUT (p < 0.001), CDKN2A (p = 0.547), or SMAD4 (p = 0.064) compared to patients with wild-type KRAS/TP53, CDKN2A, or SMAD4. Conclusions We exhibited real-world genetic traits and new alterations in Chinese individuals with cancer of the pancreas, which might have interesting implications for future individualized therapy and medication development.
The relationship between endogenous oxytocin and vasopressin levels and the Prader-Willi syndrome behaviour phenotype

Background Oxytocin and vasopressin systems are altered in Prader Willi syndrome (PWS). However, investigations into endogenous oxytocin and vasopressin levels as well as clinical trials evaluating the effect of exogenous oxytocin on PWS symptoms have had mixed results. It is also unknown whether endogenous oxytocin and vasopressin levels are associated with certain PWS behaviours. Method We compared plasma oxytocin and vasopressin and saliva oxytocin levels in 30 adolescents and adults with PWS to 30 typically developing age-matched controls. We also compared neuropeptide levels between gender and genetic subtypes within the PWS cohort and examined the relationship between neuropeptide levels and PWS behaviours. Results While we did not measure a group difference in plasma or saliva oxytocin levels, plasma vasopressin was significantly lower in individuals with PWS compared to controls. Within the PWS cohort, saliva oxytocin levels were higher in females compared to males and individuals with the mUPD compared to the deletion genetic subtype. We also found the neuropeptides correlated with different PWS behaviours for males and females and for genetic subtypes. For the deletion group, higher plasma and saliva oxytocin levels were related to fewer behaviour problems. For the mUPD group, higher plasma vasopressin levels were related to more behaviour problems. Conclusion These findings support existing evidence of a vasopressin system defect in PWS and for the first time identify potential differences in the oxytocin and vasopressin systems across PWS genetic subtypes.
Failure to decrease HbA1c levels following TB treatment is associated with elevated Th1/Th17 CD4+ responses

Introduction The rising global burden of metabolic disease impacts the control of endemic tuberculosis (TB) in many regions, as persons with diabetes mellitus (DM) are up to three times more likely to develop active TB than those without DM. Active TB can also promote glucose intolerance during both acute infection and over a longer term, potentially driven by aspects of the immune response. Identifying patients likely to have persistent hyperglycemia following TB treatment would enable closer monitoring and care, and an improved understanding of underlying immunometabolic dysregulation. Methods We measured the relationship of plasma cytokine levels, T cell phenotypes and functional responses with the change in hemoglobin A1c (HbA1c) before and after treatment of pulmonary TB in a prospective observational cohort in Durban, South Africa. Participants were stratified based on stable/increased HbA1c (n = 16) versus decreased HbA1c (n = 46) levels from treatment initiation to 12 month follow-up. Results CD62 P-selectin was up- (1.5-fold) and IL-10 downregulated (0.85-fold) in plasma among individuals whose HbA1c remained stable/increased during TB treatment. This was accompanied by increased pro-inflammatory TB-specific IL-17 production (Th17). In addition, Th1 responses were upregulated in this group, including TNF-α production and CX3CR1 expression, with decreased IL-4 and IL-13 production. Finally, the TNF-α+ IFNγ+ CD8+ T cells were associated with stable/increased HbA1c. These changes were all significantly different in the stable/increased HbA1c relative to the decreased HbA1c group. Discussion Overall, these data suggest that patients with stable/increased HbA1c had an increased pro-inflammatory state. Persistent inflammation and elevated T cell activity in individuals with unresolved dysglycemia following TB treatment may indicate failure to fully resolve infection or may promote persistent dysglycemia in these individuals, and further studies are needed to explore potential mechanisms.
Neuro-PASC is characterized by enhanced CD4+ and diminished CD8+ T cell responses to SARS-CoV-2 Nucleocapsid protein

Introduction Many people with long COVID symptoms suffer from debilitating neurologic post-acute sequelae of SARS-CoV-2 infection (Neuro-PASC). Although symptoms of Neuro-PASC are widely documented, it is still unclear whether PASC symptoms impact virus-specific immune responses. Therefore, we examined T cell and antibody responses to SARS-CoV-2 Nucleocapsid protein to identify activation signatures distinguishing Neuro-PASC patients from healthy COVID convalescents. Results We report that Neuro-PASC patients exhibit distinct immunological signatures composed of elevated CD4+ T cell responses and diminished CD8+ memory T cell activation toward the C-terminal region of SARS-CoV-2 Nucleocapsid protein when examined both functionally and using TCR sequencing. CD8+ T cell production of IL-6 correlated with increased plasma IL-6 levels as well as heightened severity of neurologic symptoms, including pain. Elevated plasma immunoregulatory and reduced pro-inflammatory and antiviral response signatures were evident in Neuro-PASC patients compared with COVID convalescent controls without lasting symptoms, correlating with worse neurocognitive dysfunction. Discussion We conclude that these data provide new insight into the impact of virus-specific cellular immunity on the pathogenesis of long COVID and pave the way for the rational design of predictive biomarkers and therapeutic interventions.