Miracle-dz/UniFAR-FTUs huggingface dataset:
Mass Spectrometric Analysis of Glycosphingolipid Antigens

Glycosphingolipids (GSL's) belong to the glycoconjugate class of biomacromolecules, which bear structural information for significant biological processes such as embryonic development, signal transduction, and immune receptor recognition1-2. They contain complex sugar moieties in the form of isomers, and lipid moieties with variations including fatty acyl chain length, unsaturation, and hydroxylation. Both carbohydrate and ceramide portions may be basis of biological significance. For example, tri-hexosylceramides include globotriaosylceramide (Galα4Galβ4Glcβ1Cer) and isoglobotriaosylceramide (Galα3Galβ4Glcβ1Cer), which have identical molecular masses but distinct sugar linkages of carbohydrate moiety, responsible for completely different biological functions3-4. In another example, it has been demonstrated that modification of the ceramide part of alpha-galactosylceramide, a potent agonist ligand for invariant NKT cells, changes their cytokine secretion profiles and function in animal models of cancer and auto-immune diseases5. The difficulty in performing a structural analysis of isomers in immune organs and cells serve as a barrier for determining many biological functions6. Here, we present a visualized version of a method for relatively simple, rapid, and sensitive analysis of glycosphingolipid profiles in immune cells7-9. This method is based on extraction and chemical modification (permethylation, see below Figure 5A, all OH groups of hexose were replaced by MeO after permethylation reaction) of glycosphingolipids10-15, followed by subsequent analysis using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF/MS) and ion trap mass spectrometry. This method requires 50 million immune cells for a complete analysis. The experiments can be completed within a week. The relative abundance of the various glycosphingolipids can be delineated by comparison to synthetic standards. This method has a sensitivity of measuring 1% iGb3 among Gb3 isomers, when 2 fmol of total iGb3/Gb3 mixture is present9. Ion trap mass spectrometry can be used to analyze isomers. For example, to analyze the presence of globotriaosylceramide and isoglobtriaosylceramide in the same sample, one can use the fragmentation of glycosphingolipid molecules to structurally discriminate between the two (see below Figure 5). Furthermore, chemical modification of the sugar moieties (through a permethylation reaction) improves the ionization and fragmentation efficiencies for higher sensitivity and specificity, and increases the stability of sialic acid residues. The extraction and chemical modification of glycosphingolipids can be performed in a classic certified chemical hood, and the mass spectrometry can be performed by core facilities with ion trap MS instruments.
The Fundamental Physics of Directive Beaming at Microwave and Optical Frequencies and the Role of Leaky Waves

This review paper summarizes various aspects of directive beaming and explains these aspects in terms of leaky waves. Directive beaming occurs in antenna design where a narrow beam is obtainable by using fairly simple planar structures excited by a single source. These structures include Fabry-Pérot cavity structures as well as metamaterial structures made from artificial low-permittivity media. Directive beaming also occurs in the optical area where it has been observed that highly directive beams can be produced from small apertures in a metal film when an appropriate periodic patterning is placed on the film. One aspect that these phenomena all have in common is that they are due to the excitation of one or more weakly attenuated leaky waves, the radiation from which forms the directive beam. This is established in each case by examining the role of the leaky waves in determining the near-field on the aperture of the structure and the far-field radiation pattern of the structure.
Performance of Adaptive Maximum Torque Per Amp Control at Multiple Operating Points for Induction Motor Drives

The highly efficient operation of induction motors has been studied in the past years. Among the many attempts made to obtain highly efficient operation, Maximum Torque Per Amp (MTPA) controls in induction motor drives were proposed. This method enables induction motor drives to operate very efficiently since it achieves the desired torque with the minimal stator current. This is because the alternate qd induction motor model (AQDM) is a highly accurate mathematical model to represent the dynamic characteristics of induction motors. However, it has been shown that the variation of the rotor resistance degrades the performance of the MTPA control significantly, thus leading to its failure to satisfy the maximum torque per amp condition. To take into consideration the mismatch between the actual value of the rotor resistance and its parameter value in the design of the control strategy, an adaptive MTPA control was proposed. In this work, this adaptive MTPA control is investigated in order to achieve the desired torque with the minimum stator current at multiple operating points. The experimental study showed that (i) the desired torque was accurately achieved even though there was a deviation of the order of 5% from the commanded torque value at a torque reference of 25 Nm (tracking performance), and (ii) the minimum stator current for the desired torque (maximum torque per amp condition) was consistently satisfied at multiple operating points, as the rotor temperature increased. 요 약 유도전동기를 고효율로 제어하기 위한 다양한 연구가 진행되어 왔다. 그 중에서 단위전류당 최대토크 제어기는 최소한의 고정자 전류로 원하는 토크를 제공하기 때문에 유도전동기 드라이브에서 고효율의 동작을 제공한다. 이는 유도전 동기를 수학적으로 정밀하게 표현하는 대안모델을 기반으로 제어기가 설계되었기 때문이다. 그러나, 온도 변화에 따른 회전 자 저항의 변이는 대안모델의 파라미터와 실제의 유도전동기의 파라미터의 불일치가 발생하여 단위전류당 최대토크 성능을 심각하게 저해하고 단위전류당 최대토크 제어 조건을 만족하지 못하게 하게 있다. 이러한 유도전동기의 운전시에 발생하는 열적 상승으로 인한 파라미터 값의 변화를 고려하는 단위전류당 최대토크적응 제어기가 제안되었다. 본 논문에서는 단위전 류당 최대토크적응 제어기가 다수의 운전영역에서도 최소의 고정자 전류로 원하는 토크를 성취하는지를 검토하였다. 실험을 통한 연구에서 회전자의 온도가 증가하더라도 다수의 운전영역에서 25Nm의 토크 명령에서 5%의 차이가 존재하더라도 토크 명령을 정확하게 추구하고 또한, 원하는 토크를 최소한의 고정자 전류로 얻어짐을 확인함으로써 단위전류당 최대토크적응
Whole-Body Vibration Training and Its Application to Age-Related Performance Decrements: An Exploratory Analysis

Abstract Hawkey, A, Griffiths, K, Babraj, J, and Cobley, JN. Whole-body vibration training and its application to age-related performance decrements: an exploratory analysis. J Strength Cond Res 30(2): 555–560, 2016—Middle age is associated with a pronounced decline in power and flexibility. Whilst whole-body vibration training (WBVT) improves performance in a range of populations, whether WBVT can improve muscle power and flexibility in a middle-aged population is not known. The present study aimed to determine the influence of 5 weeks progressive WBVT in middle-aged (45–55 years) and younger (20–30 years) recreationally active females. Participants in each age group were randomly allocated to an intervention (WBVT) or control group. The WBVT groups trained for 5 weeks on a vibration platform, while the control groups performed identical exercises, with no vibration. Prior to, and after, the 5-week study vertical countermovement jump (VCMJ) and range of motion (ROM) performance were measured. WBVT significantly (p = 0.001) improved VCMJ performance when compared to the control groups. This improvement was significantly (p = 0.001) greater in the middle-aged compared with the younger WBVT group. WBVT significantly (p = 0.001) improved ROM irrespective of age. Taken together, these results suggest that WBVT can off-set age related performance decrements, which has therapeutic implications for musculoskeletal aging. Therefore, WBVT could be undertaken to minimise age-related performance deterioration in middle-aged female populations.
Epidemiology of viral acute lower respiratory infections in a community-based cohort of rural north Indian children

Background In India, community-based acute lower respiratory infections (ALRI) burden studies are limited, hampering development of prevention and control strategies. Methods We surveyed children <10 years old at home weekly from August 2012-August 2014, for cough, sore throat, rhinorrhoea, ear discharge, and shortness of breath. Symptomatic children were assessed for ALRI using World Health Organization definitions. Nasal and throat swabs were obtained from all ALRI cases and asymptomatic controls and tested using polymerase chain reaction for respiratory syncytial virus (RSV), human metapneumovirus (hMPV), parainfluenza viruses (PIV), and influenza viruses (IV). We estimated adjusted odds ratios (aOR) using logistic regression to calculate etiologic fractions (EF). We multiplied agent-specific ALRI incidence rates by EF to calculate the adjusted incidence as episodes per child-year. Results ALRI incidence was 0.19 (95% confidence interval (CI) = 0.18-0.20) episode per child-year. Association between virus and ALRI was strongest for RSV (aOR = 15.9; 95% CI = 7.3-34.7; EF = 94%) and least for IV (aOR = 4.6; 95% CI = 2.0-10.6; EF = 78%). Adjusted agent-specific ALRI incidences were RSV (0.03, 95% CI = 0.02-0.03), hMPV (0.02, 95% CI = 0.01-0.02), PIV (0.02, 95% CI = 0.01-0.02), and IV (0.01, 95% CI = 0.01-0.01) episode per child-year. Conclusions ALRI among children in rural India was high; RSV was a significant contributor.
Relation Between Quality of Life and Morbidity and Mortality in COPD Patients: Two-Year Follow-Up Study

ABSTRACT Quality of life (QoL) is being recognized as an important outcome when evaluating chronic obstructive pulmonary disease (COPD) patients. This study aims at identifying the relation between QoL parameters and mortality and morbidity in COPD patients by using the St. George Respiratory Questionnaire (SGRQ). In this prospective study, 251 COPD patients as defined by American Thoracic Society (ATS) criteria were included. A total of 218 patients (86.85%) were male and mean age was 65.55 years. A pulmonary function test (PFT) and SGRQ were performed at the beginning, first, and second years. During a two-year follow-up, the first exacerbation day, the number of exacerbations and intubations, the number and duration of hospitalizations, hospitalizations in an intensive care unit, and exitus day were recorded. When the correlation between FEV1, SGRQ scores, and these parameters was investigated, there was significant correlation between these parameters, and this correlation was more significant in SGRQ scores than FEV1 (Pearson correlation test). The activity score of SGRQ was found to be more useful than other scores (Cox regression analysis). Not only PFT but also QoL questionnaires are useful in determining the prognosis of COPD. QoL questionnaires provide a valid and standardized estimate of the overall impact of COPD, and can complement spirometric measurements of baseline assessment of patients in routine practice.
Clinical characteristics and disability in patients with knee osteoarthritis: real world experience from Bulgaria

Objectives Although knee osteoarthritis (KOA) is a leading cause of impaired functioning among older adults globally, little is still known about the complex mechanisms of disability accumulation in these patients. The aim of the study was to analyze the clinical parameters of patients with KOA in a Bulgarian population and to determine which of these clinical characteristics define disability to the greatest extent. Material and methods Patients aged 40–80 years with symptomatic KOA were included. The assessment tools for pain, clinical disease severity, and disability were the pain visual analogue scale (VAS) and disease-specific questionnaires: Algofunctional Index of Lequesne, Western Ontario and McMaster Universities OA Index (WOMAC), and the Health Assessment Questionnaire-Disability Index (HAQ-DI), respectively. Radiographs of the knees were obtained and graded according to the Kellgren-Lawrence (KL) system. Results One hundred and thirty-two patients (81% women) participated in the study. The median values of VAS (mm), WOMAC, Lequesne, and HAQ-DI scores were 52, 37.5, 11, 0.88, respectively. Men had milder disease, resulting in lower VAS, WOMAC, Lequesne, and HAQ-DI scores and less structural damage compared to women (p < 0.05). WOMAC index correlated positively with age of the patients but not with duration of the complaints. Patients with severe and very severe pain did not differ in their HAQ-DI, disease severity and KL grading. WOMAC physical function score and Lequesne index were independent predictors for the HAQ-DI in patients with KOA. Conclusions Bulgarian patients with KOA had moderate disability which showed a strong relationship with physical function of WOMAC and disease severity. Multiple layers of causality coexist to determine the knee pain in Bulgarian patients with KOA.
Clinical Decision Support Functions and Digitalization of Clinical Documents of Electronic Medical Record Systems

Objectives The objective of this study was to investigate the clinical decision support (CDS) functions and digitalization of clinical documents of Electronic Medical Record (EMR) systems in Korea. This exploratory study was conducted focusing on current status of EMR systems. Methods This study used a nationwide survey on EMR systems conducted from July 25, 2018 to September 30, 2018 in Korea. The unit of analysis was hospitals. Respondents of the survey were mainly medical recorders or staff members in departments of health insurance claims or information technology. This study analyzed data acquired from 132 hospitals that participated in the survey. Results This study found that approximately 80% of clinical documents were digitalized in both general and small hospitals. The percentages of general and small hospitals with 100% paperless medical charts were 33.7% and 38.2%, respectively. The EMR systems of general hospitals are more likely to have CDS functions of warnings regarding drug dosage, reminders of clinical schedules, and clinical guidelines compared to those of small hospitals; this difference was statistically significant. For the lists of digitalized clinical documents, almost 93% of EMR systems in general hospitals have the inpatient progress note, operation records, and discharge summary notes digitalized. Conclusions EMRs are becoming increasingly important. This study found that the functions and digital documentation of EMR systems still have a large gap, which should be improved and made more sophisticated. We hope that the results of this study will contribute to the development of more sophisticated EMR systems.
Development of Artificial Intelligence to Support Needle Electromyography Diagnostic Analysis

Objectives This study proposes a method for classifying three types of resting membrane potential signals obtained as images through diagnostic needle electromyography (EMG) using TensorFlow-Slim and Python to implement an artificial-intelligence-based image recognition scheme. Methods Waveform images of an abnormal resting membrane potential generated by diagnostic needle EMG were classified into three types—positive sharp waves (PSW), fibrillations (Fibs), and Others—using the TensorFlow-Slim image classification model library. A total of 4,015 raw waveform data instances were reviewed, with 8,576 waveform images subsequently collected for training. Images were learned repeatedly through a convolutional neural network. Each selected waveform image was classified into one of the aforementioned categories according to the learned results. Results The classification model, Inception v4, was used to divide waveform images into three categories (accuracy = 93.8%, precision = 99.5%, recall = 90.8%). This was done by applying the pretrained Inception v4 model to a fine-tuning method. The image recognition model was created for training using various types of image-based medical data. Conclusions The TensorFlow-Slim library can be used to train and recognize image data, such as EMG waveforms, through simple coding rather than by applying TensorFlow. It is expected that a convolutional neural network can be applied to image data such as the waveforms of electrophysiological signals in a body based on this study.
Revisiting the Arm Debug Facility for OS Kernel Security

Hardware debugging facilities, such as watchpoints, have been used for software development and analysis. In this paper, we expanded the use of watchpoints as a hardware security primitive for enhancing the runtime security of mobile devices. By analyzing the watchpoints in detail, we derived useful watchpoint properties that can be exploited to build security applications. Based on our analysis, we designed example applications for hardening the OS kernel by exploiting watchpoints. The proposed applications were implemented on a Juno development board with 64-bit ARM architecture (ARMv8). Hardening the kernel by fully enabling the proposed schemes was found to impose reasonable overhead, i.e., 3% with SPEC CPU2006.
No Compromises: Secure NVM with Crash Consistency, Write-Efficiency and High-Performance

Data encryption and authentication are essential for secure NVM. However, the introduced security metadata needs to be atomically written back to NVM along with data, so as to provide crash consistency, which unfortunately incurs high overhead. To support fine-grained data protection without compromising the performance, we propose cc-NVM. It firstly proposes an epoch-based mechanism to aggressively cache the security metadata in CPU cache while retaining the consistency of them in NVM. Deferred spreading is also introduced to reduce the calculating overhead for data authentication. Leveraging the hidden ability of data HMACs, we can always recover the consistent but old security metadata to its newest version. Compared to Osiris, a state-of-the-art secure NVM, cc-NVM improves performance by 20.4% on average. When the system crashes, instead of dropping all the data due to malicious attacks, cc-NVM is able to detect and locate the exact tampered data while only incurring extra write traffic by 29.6% on average.
Tighter Dimensioning of Heterogeneous Multi-Resource Autonomous CPS with Control Performance Guarantees

In modern autonomous systems, there is typically a large number of connected components realizing complex functionalities. For example, in autonomous vehicles (AVs), there are tens of millions of lines of code implemented on hundreds of sensors, controllers, and actuators. AVs have been deployed, mostly in trials and restricted environments, showing that substantial progress has been made in functionality development. However, they are still faced with two major challenges: (i) performance guarantee of safety-critical functions under all possible scenarios; (ii) functionality implementation with limited resources. These two challenges are conflicting because safety guarantees necessitate a worst-case analysis that is often very pessimistic for complex hardware/software systems, and thus require more resources. To address this, we study an abstraction of a heterogeneous cyber-physical system architecture consisting of a mix of high- and low-quality resources, such as time- and eventtriggered resources, or wired and wireless resources. We show that by properly managing such a mix of resources and formulating a formal verification (model checking) problem, it is possible to tightly dimension the high-quality resource to the minimum (50% in certain cases) while providing control performance guarantees.
Dynamics of Myosin Heavy Chain Gene Regulation in Slow Skeletal Muscle

The evolutionarily conserved order of the skeletal muscle myosin heavy chain (MHC) genes and their close tandem proximity on the same chromosome are intriguing and may be important for their coordinated regulation. We investigated type II MHC gene regulation in slow-type muscle fibers undergoing a slow to fast MHC transformation in response to inactivity, 7 days after spinal cord isolation (SI) in rats. We examined the transcriptional products of both the sense and antisense strands across the IIa-IIx-IIb MHC gene locus. A strand-specific reverse transcription (RT)-PCR approach was utilized to study the expression of the mRNA, the primary transcript (pre-mRNA), the antisense RNA overlapping the MHC genes, and both the intergenic sense and antisense RNAs. Results showed that the mRNA and pre-mRNA of each MHC had a similar response to SI, suggesting regulation of these genes at the transcriptional level. In addition, we detected previously unknown antisense strand transcription that produced natural antisense transcripts (NATs). RT-PCR mapping of the RNA products revealed that the antisense activity resulted in the formation of three major products: aII, xII, and bII NATs (antisense products of the IIa, IIx, and IIb genes, respectively). The aII NAT begins in the IIa-IIx intergenic region in close proximity to the IIx promoter, extends across the 27-kb IIa MHC gene, and continues to the IIa MHC gene promoter. The expression of the aII NAT was significantly up-regulated in muscles after SI, was negatively correlated with IIa MHC gene expression, and was positively correlated with IIx MHC gene expression. The exact role of the aII NAT is not clear; however, it is consistent with the inhibition of IIa MHC gene transcription. In conclusion, NATs may mediate cross-talk between adjacent genes, which may be essential to the coordinated regulation of the skeletal muscle MHC genes during dynamic phenotype shifts.
Ab Initio Study of Lowest-Energy Conformers of Lewis X (Lex) Trisaccharide

This paper presents the first ab initio conformational study of the Gal-β-1,4-[Fuc-α-1,3]-GlcNAc-β-OCH3 and Gal-β-1,4-[Fuc-α-1,3]-GlcNAc-β-OH trisaccharides (Lewis x) in the gas phase. Their lowest-energy conformers were selected first by the MM2*-SUMM conformational search technique. MM2* relative energies do not follow the same order for the two similar compounds. The molecular geometries and energies of the lowest-energy rotamers (7 of the acetal and 11 of the hemiacetal) were further analyzed at the HF/6-31G(d) level of theory. The ab initio method yields the same energetic order for the rotamers of the two molecules with considerably larger energetic differences for the first 7 rotamers: the MM2* method provides 0.3−0.5 kcal/mol, whereas the HF/6-31G(d) method provides 4.5 kcal/mol. In the most stable MM2* structures the hydrogen-bonded chains of galactose (in counterclockwise direction) and fucose (in clockwise direction) are not connected. The Gal(O6H) is a hydrogen bond donor (in clockwise direct.
A Hybrid Agent-based Design Methodology for Dynamic Cross-layer Reliability in Heterogeneous Embedded Systems

Technology scaling and architectural innovations have led to increasing ubiquity of embedded systems across applications with widely varying and often constantly changing performance and reliability specifications. However, the increasing physical fault-rates in electronic systems have led to single-layer reliability approaches becoming infeasible for resource-constrained systems. Dynamic Cross-layer reliability (CLR) provides scope for efficient adaptation to such QoS variations and increasing unreliability. We propose a design methodology for enabling QoS-aware CLR-integrated run-time adaptation in heterogeneous MPSoC-based embedded systems. Specifically, we propose a combination of reconfiguration cost-aware optimization at design-time and an agent-based optimization at run-time. We report a reduction of up to 51% and 37% in average reconfiguration cost and average energy consumption respectively over state-of-the-art approaches.