Miracle-dz/UniFAR-FTUs huggingface dataset:
Identification of Boolean Network Models From Time Series Data Incorporating Prior Knowledge

Motivation: Mathematical models take an important place in science and engineering. A model can help scientists to explain dynamic behavior of a system and to understand the functionality of system components. Since length of a time series and number of replicates is limited by the cost of experiments, Boolean networks as a structurally simple and parameter-free logical model for gene regulatory networks have attracted interests of many scientists. In order to fit into the biological contexts and to lower the data requirements, biological prior knowledge is taken into consideration during the inference procedure. In the literature, the existing identification approaches can only deal with a subset of possible types of prior knowledge. Results: We propose a new approach to identify Boolean networks from time series data incorporating prior knowledge, such as partial network structure, canalizing property, positive and negative unateness. Using vector form of Boolean variables and applying a generalized matrix multiplication called the semi-tensor product (STP), each Boolean function can be equivalently converted into a matrix expression. Based on this, the identification problem is reformulated as an integer linear programming problem to reveal the system matrix of Boolean model in a computationally efficient way, whose dynamics are consistent with the important dynamics captured in the data. By using prior knowledge the number of candidate functions can be reduced during the inference. Hence, identification incorporating prior knowledge is especially suitable for the case of small size time series data and data without sufficient stimuli. The proposed approach is illustrated with the help of a biological model of the network of oxidative stress response. Conclusions: The combination of efficient reformulation of the identification problem with the possibility to incorporate various types of prior knowledge enables the application of computational model inference to systems with limited amount of time series data. The general applicability of this methodological approach makes it suitable for a variety of biological systems and of general interest for biological and medical research.
Mechanical characterization comparison as flip-chip package to fan-out package

In this study, the mechanical responses including warpage and die stress were compared between different packages, naming flip-chip, core-less flip-chip, core-less molded flip-chip, fan-out, exposed-die fan-out, and back-side protective fan-out. All packages had the same die size with 8×8 mm2, the same package size with 15×15 mm2, and the same Cu layers with 4L. The finite element method (FEM) was conducted to simulate the warpage and the stress intensity factor (SIF) of the die. The strategy of this study was to compare the mechanical responses of each package, and to show the warpage and SIF ratios. Then the improvements of mechanical responses by changing component thicknesses were compared. Finally, the improvement suggestions were provided.
Design Method for Multiband Filters With Compact Configuration in Substrate Integrated Waveguide

In this paper, a design method for multiband bandpass filters with compact configuration in substrate integrated waveguide is proposed by combining the single-band/dual-band synthesis method and the multimode resonator theory. The designed filters could generate multiple filtering passbands without expanding their entire physical size. In addition, all the passbands could be efficiently synthesized and designed with any prescribed order in theory, which has been rarely reported in multiband filters, especially in the design of quad-band filters. As examples, one third-order quad-band filter and one third-order tri-band filter are designed, fabricated, and measured. Good agreement is attained between their simulated and measured S-parameters, and both the two sets of results have verified the feasibility of the proposed design method and attractive performances of the designed multiband filters.
Functional and Evolutionary Characterization of the CONSTANS-like Family in Lilium[REPLACEMENT CHARACTER]formolongi

Lilium × formolongi is a facultative long day (LD) plant. Aiming to dissect the molecular regulation of the photoperiodic pathway, largely unknown in Lilium, we explored the CONSTANS/FLOWERING LOCUS T (CO/FT) module, a major regulatory factor in the external coincidence model of photoperiodic flowering pathway in lily. We identified eight CONSTANS-LIKE (COL) family members in L. × formolongi, which could be divided into three types, according to their zinc-finger (B-box) protein domains. Type I included only LfCOL5, containing two B-box motifs. Type II contained six LfCOLs members that had only one B-box motif. Type III solely contained LfCOL9 that showed a normal B-box and a second divergent B-box motif. Phylogenic analyses revealed that LfCOL5 was the closest to the Arabidopsis CO. LfCOL5, LfCOL6 and LfCOL9 were up-regulated at the flowering induction stage under LD, coinciding with an increase in LfFT1 expression. LfCOL5, LfCOL6 and LfCOL9 also showed obvious diurnal expression pattern for three days under LD. However, under short day (SD) conditions, LfCOL5, LfCOL6 and LfCOL9 expression patterns were variable and complex, with regard to the developmental stages and circadian rhythm. LfCOL5, LfCOL6 and LfCOL9 complemented the late flowering phenotype of the co mutant in Arabidopsis. Taken together, the results suggest that LfCOL5, LfCOL6 and LfCOL9 are involved in triggering flowering induction under LD. LfCOL6 and LfCOL9 belong to different types than functional COL homologs in other plant species, illustrating the variation in phylogeny, evolution and gene function among LfCOL family members.
Heterogranular multivariate analytics for detecting and controlling the root causes of the mismatching machines in semiconductor manufacturing

In all manufacturing industries, parallel machines/chambers at a single production area are expected to perform identically and, most importantly, to yield similar product quality. However, this is usually not the case in real practice, especially when it is a highly complex industry as is the case for semiconductor fabrication. In this paper, a systematic approach is proposed to detect the root causes of machine/chamber mismatching in real time by exploiting all the available data, such as product measurements, machine sensor readings and maintenance data.
Surgical Outcomes of Minimally Invasive Stabilization for Spinal Fractures in Patients with Ankylosing Spinal Disorders

Study Design A retrospective study. Purpose To evaluate the clinical and radiological outcomes of ankylosing spinal disorder (ASD) patients with spinal fractures treated by minimally invasive stabilization (MISt) using percutaneous pedicle screws (PPSs). Overview of Literature ASDs, such as ankylosing spondylitis (AS) and diffuse idiopathic skeletal hyperostosis (DISH), increase susceptibility to spinal fractures because of extremely decreased spinal flexibility. Such fractures tend to be unstable and, consequently, should be treated with multiple-segmental internal fixation. However, conventional internal fixation procedures can severely damage the soft tissue, resulting in severe hemorrhage. Therefore, MISt is the preferred approach to treat spinal fractures in ASD patients. Methods Nine ASD patients (four males and five females; three AS and six DISH patients) with spinal fractures who were treated by MISt using PPSs, were reviewed from April 2009 to August 2016. One patient died of aspiration pneumonia during follow-up (FU), and the remaining eight patients underwent clinical and radiological evaluation. Results The mean age at surgery was 79.6 years (range, 68–95 years). The mean duration of postoperative FU was 14.2 months (range, 3–30 months). All treated fractures were anterior and posterior element injuries with distraction. Three patients presented delayed onset preoperative neurological deficit following trauma. The mean operation time was 179.6 minutes (range, 92–340 minutes). The mean hemorrhage was 103.6 mL (range, unquantifiable to 480 mL). Radiological evaluations at FU showed preservation of the acceptable postoperative correction of the fractured vertebra, as there were no re-collapses of the fractured vertebrae during FU. Conclusions ASD patients must be acknowledged as highly susceptible to unstable spinal fractures, even after relatively mild trauma. MISt using PPSs may be an effective treatment for spinal fractures in such patients.
Oral Antidiabetic Agents The Emergence of a-Glucosidase Inhibitors

Hyperglycaern ia in patients with non-insulin-dependent diabetes mellitus (NIDDM) results from impaired insulin action and/or deficient insulin secretion, These abnormalities lead to increased hepatic glucose production, the primary cause of fasting hyperglycaemia, and decreased peripheral glucose uptake, the major mechanism responsible for postprandial hyperglycaemia . Hyperglycaemia in patients with NIDDM can be decreased by several ditTerent mechanisms: (I) a decrease in nutrient ingestion; (2) an increase in insulin secretion; (3) a decrease in hepatic glucose production; (4) an increase in peripheral glucose uptake . Oral agents used to treat NIDDM operate through I or more of the above mechanisms. a-Glucosidase inhibitors, a new class of drugs that delay carbohydrate digestion and absorption, reduce postprandial glycaemic rises by about 3 mrnol /L . Metformin decreases fasting and postprandial hyperglycaemia through increasing glucose uptake and perhaps decreasing appetite. Sulphonylureas lower hyperglycaemia by increasing insulin secretion and to a lesser degree potentiating insulin action on the liver and peripheral tissues. a-Glucosidase inhibitors are particularly useful as primary therapy for patients with mild to moderate hyperglycaemia and in those patients who may be at risk for hypoglycaemia or lactic acidosis. Sulphonylureas are indicated for the more severely hyperglycaemic NIDDM patients who are not yet candidates for insulin therapy. Metformin is useful in obese moderately hyperglycaemic NIDDM patients. These oral agents can be used in combination to give better glycaemic control than is possible with each alone.
Activating Transcription Factor 4 (ATF4) Regulates Neuronal Activity by Controlling GABABR Trafficking

Activating Transcription Factor 4 (ATF4) has been postulated as a key regulator of learning and memory. We previously reported that specific hippocampal ATF4 downregulation causes deficits in synaptic plasticity and memory and reduction of glutamatergic functionality. Here we extend our studies to address ATF4's role in neuronal excitability. We find that long-term ATF4 knockdown in cultured rat hippocampal neurons significantly increases the frequency of spontaneous action potentials. This effect is associated with decreased functionality of metabotropic GABAB receptors (GABABRs). Knocking down ATF4 results in significant reduction of GABABR-induced GIRK currents and increased mIPSC frequency. Furthermore, reducing ATF4 significantly decreases expression of membrane-exposed, but not total, GABABR 1a and 1b subunits, indicating that ATF4 regulates GABABR trafficking. In contrast, ATF4 knockdown has no effect on surface expression of GABABR2s, several GABABR-coupled ion channels or β2 and γ2 GABAARs. Pharmacologic manipulations confirmed the relationship between GABABR functionality and action potential frequency in our cultures. Specifically, the effects of ATF4 downregulation cited above are fully rescued by transcriptionally active, but not by transcriptionally inactive, shRNA-resistant, ATF4. We previously reported that ATF4 promotes stabilization of the actin-regulatory protein Cdc42 by a transcription-dependent mechanism. To test the hypothesis that this action underlies the mechanism by which ATF4 loss affects neuronal firing rates and GABABR trafficking, we downregulated Cdc42 and found that this phenocopies the effects of ATF4 knockdown on these properties. In conclusion, our data favor a model in which ATF4, by regulating Cdc42 expression, affects trafficking of GABABRs, which in turn modulates the excitability properties of neurons. SIGNIFICANCE STATEMENT GABAB receptors (GABABRs), the metabotropic receptors for the inhibitory neurotransmitter GABA, have crucial roles in controlling the firing rate of neurons. Deficits in trafficking/functionality of GABABRs have been linked to a variety of neurological and psychiatric conditions, including epilepsy, anxiety, depression, schizophrenia, addiction, and pain. Here we show that GABABRs trafficking is influenced by Activating Transcription Factor 4 (ATF4), a protein that has a pivotal role in hippocampal memory processes. We found that ATF4 downregulation in hippocampal neurons reduces membrane-bound GABABR levels and thereby increases intrinsic excitability. These effects are mediated by loss of the small GTPase Cdc42 following ATF4 downregulation. These findings reveal a critical role for ATF4 in regulating the modulation of neuronal excitability by GABABRs.
Combined Laminoplasty and Posterior Fusion for Cervical Spondylotic Myelopathy Treatment: A Literature Review

Study Design A literature review. Purpose To explore the utility of laminoplasty in combination with instrumented fusion, with a focus on neurological outcomes and changes in kyphotic deformity. Overview of Literature Management of cervical spondylotic myelopathy (CSM) to reduce morbidity within the neurosurgical population. Methods A US National Library of Medicine PubMed search was conducted for manuscripts pertaining to cervical laminoplasty and fusion for the management of CSM. Several relevant studies were shortlisted for review, and the bibliographies of the articles were searched for additional references. The search was limited to human studies, English-language literature, and reports on more than one patient. Results Combined laminoplasty and fusion was found to provide at least comparable, if not superior, neurological outcomes in specific patient populations with CSM. The Japanese Orthopedic Association scores, local kyphosis, and C2–C7 angle have been reviewed in several manuscripts, and improvement in each of these categories was found with laminoplasty and fusion. Conclusions The treatment of CSM necessitates an individualized approach based on the pathoanatomical variation. Laminoplasty and fusion can be appropriately used for patients with CSM in a setting of local kyphotic deformity, ossification of the posterior longitudinal ligament, associated segmental instability, and the need for strong stabilization.
CAN IT BE REVERSED ? A NEW BIOLOGICAL TREATMENT TECHNIQUE FOR TREATING PATIENTS WITH MODERATE TO ADVANCED GONARTHROSIS

BÜLENT KILIÇ1, MURAT DEMIROĞLU2, FEYZA ÜNLÜ ÖZKAN3, MEHMET SALIH SÖYLEMEZ4, İSMAIL TÜRKMEN5, YAVUZ SAĞLAM6, KORHAN ÖZKAN7 1Istanbul Gelişim University, Department of Health Sciences, Orthopaedic Surgeon, Istanbul, Turkey 2Istanbul Medeniyet University, Goztepe Training and Research Hospital, Department of Orthopaedics and Traumatology, Istanbul, Turkey 3Fatih Sultan Mehmet Training and Research Hospital, Department of Physical Therapy and Rehabilitation, Istanbul, Turkey 4Bingöl State Hospital, Department of Orthopaedics and Traumatology, Bingöl, Turkey 5Beykoz State Hospital, Department of Orthopaedics and Traumatology, Istanbul, Turkey 6Biruni University, Faculty of Medicine, Department of Orthopaedics and Traumatology, Istanbul, Turkey 7Istanbul Medeniyet University, Faculty of Medicine, Department of Orthopaedics and Traumatology, Istanbul, Turkey
DICTIONARY-DECOMPOSITION-BASED ONE-CLASS SVM FOR UNSUPERVISED DETECTION OF ANOMALOUS TIME SERIES

In this paper, we propose a new unsupervised method to detect anomalous time series, given as little as one test data set. Particularly, the method proposed consists in an iterative procedure with two alternating steps: a dictionary learning (DL) step, to learn a pattern for the “normal” time series, and a modified One-class Support Vector Machines (OCSVM) classifier, which finds the anomalies by taking into account how much each time series deviates from the pattern found. The algorithm that arises from the original combination of these two steps represents a general framework, where any DL algorithm can be plugged in according to the model desired. When tested on two different applications (detection of shape anomalies and analysis of cardiac MRI time series), our proposed method is shown to outperform other unsupervised approaches, presenting higher detection accuracy.
Utilizing the ACC-FMCW radar for land vehicles navigation

The Global Navigation Satellite Systems (GNSS) such as Global Positioning System (GPS) are the prime land and autonomous vehicles navigation information source. However, urban canyons high rise buildings block the GPS signal. Therefore, the Inertial Navigation System (INS) or the Reduced Inertial Sensor System (RISS) are utilized as an alternative source of the navigation information. The RISS is able to produce a full navigation solution using less number of sensors and calculations. Dramatically, the RISS solution drifts over time as the INS system. The integration between the GPS and the RISS is mitigating each system drawbacks. However, during the GPS outage periods, the navigation system is only depending on the inertial measurements. The RISS is utilizing the odometer/speedometer to measure the vehicle's forward speed. Many types of error affect the odometer measurements. These errors are either due to the vehicle's specifications as the differences in wheel diameters, and/or inefficient wheelbase or the road nature as wheel slips, uneven road surfaces, and/or skidding. In this paper, a Radar-based RISS system is introduced to take place the traditional RISS or INS systems. The radar unit is an essential part of the adaptive cruise control (ACC) system. Furthermore, it is capable of measuring the relative velocity and distance between the carrying and the in front vehicle to reduce collisions and increase the safety of driving. In addition, the radar measurements are not affected by the error sources that affect the odometer. The idea is to invest the ground reflection and derive the forward speed of the onboard vehicle as the ACC keep a safe distance between the cars. A novel method based on extracting the ground reflection features is introduced to obtain the onboard vehicle's speed. The obtained speed is utilized with two accelerometers and one vertical gyroscope to produce the Radar-based RISS system. The proposed system has been integrated with the GPS producing a Radar-based RISS/GPS integrated navigation system. The system has been tested on a real road trajectory in a downtown area and involved several GPS signal outages. The results show the significant capabilities of the proposed system in keeping the navigation solution drift to a minimum especially when the GPS signal is in outage compared with the traditional RISS/GPS system.
Beam Scanning Realized by Coupled Modes in a Single-Patch Antenna

In this letter, we introduce a novel beam scanning in a single-rectangular-patch antenna realized by coupled modes. The design exhibits radiated beams that scan as a function of frequency, but is different in its operation mechanism compared to a traditional leaky-wave antenna. The idea is to manipulate the phase difference between the fields at two radiating slots of the antenna to reform the beam. Metal vias are introduced to create two coupled half-mode cavities in the patch antenna. The mutual coupling between the two cavities makes the phase difference as a function of the operating frequency. The simulated beam scans from broadside to 43<inline-formula><tex-math notation="LaTeX">$^{\circ }$</tex-math></inline-formula> within the 3 dB gain band. The implemented sample realizes 4.55% bandwidth of <inline-formula><tex-math notation="LaTeX">$S_{11}$</tex-math></inline-formula> with center frequency at 5.05 GHz by measurement. The beam scans from 14<inline-formula><tex-math notation="LaTeX">$^{\circ }$</tex-math> </inline-formula> to 34<inline-formula><tex-math notation="LaTeX">$^{\circ }$</tex-math></inline-formula> within the matching band, which is confirmed by both simulation and measurement. The measured radiation efficiency within the matching band is comparable to a regular-patch antenna.
Multistate outbreak of Salmonella Paratyphi B variant L(+) tartrate(+) and Salmonella Weltevreden infections linked to imported frozen raw tuna: USA, March–July 2015

Abstract Foodborne non-typhoidal salmonellosis causes approximately 1 million illnesses annually in the USA. In April 2015, we investigated a multistate outbreak of 65 Salmonella Paratyphi B variant L(+) tartrate(+) infections associated with frozen raw tuna imported from Indonesia, which was consumed raw in sushi. Forty-six (92%) of 50 case-patients interviewed ate sushi during the week before illness onset, and 44 (98%) of 45 who specified ate sushi containing raw tuna. Two outbreak strains were isolated from the samples of frozen raw tuna. Traceback identified a single importer as a common source of tuna consumed by case-patients; this importer issued three voluntary recalls of tuna sourced from one Indonesian processor. Four Salmonella Weltevreden infections were also linked to this outbreak. Whole-genome sequencing was useful in establishing a link between Salmonella isolated from ill people and tuna. This outbreak highlights the continuing foodborne illness risk associated with raw seafood consumption, the importance of processing seafood in a manner that minimises contamination with pathogenic microorganisms and the continuing need to ensure imported foods are safe to eat. People at higher risk for foodborne illness should not consume undercooked animal products, such as raw seafood.
Sex differences in factors associated with metabolic syndrome among Korean adults without diabetes mellitus: results from the Korea National Health and Nutrition Examination Survey from 2010 to 2013

OBJECTIVES The purpose of this study was to examine sex differences in factors associated with metabolic syndrome in Korean adults without diabetes mellitus. STUDY DESIGN Cross-sectional design. METHODS The dataset of Korea National Health and Nutrition Examination Survey from 2010 to 2013 was used. Among a total of 33552 adults aged ≥30, subjects who (i) were diagnosed or had been treated for diabetes mellitus, (ii) had a fasting blood glucose level of 126 mg/dL or higher or (iii) had a glycosylated haemoglobin level of 6.5% or higher were excluded. Subjects who had anaemia or were pregnant were also excluded. Finally, 9406 subjects were included in this study. Sex differences in subjects' characteristics were assessed with Student's t-test and chi-square test. Logistic regressions were used to examine factors associated with metabolic syndrome by sex. RESULTS The prevalence of metabolic syndrome in Korean adults overall without diabetes mellitus was 12.2%. Glycosylated haemoglobin from 5.7 to 6.5 and increased body mass index were independently associated with metabolic syndrome in both men and women. Current smoking, age and age square were significantly associated with metabolic syndrome in men, whereas age and illiteracy were significantly associated with it in women. CONCLUSIONS This study confirmed that glycosylated haemoglobin and body mass index can be important indicators of metabolic syndrome in Korean adults without diabetes mellitus.