Miracle-dz/UniFAR-FTUs huggingface dataset:
One‐Bit Compressed Sensing by Linear Programming

We give the first computationally tractable and almost optimal solution to the problem of one‐bit compressed sensing, showing how to accurately recover an s‐sparse vector \input amssym $x \in {\Bbb R}^n$ from the signs of $O(s \log^2(n/s))$ random linear measurements of x. The recovery is achieved by a simple linear program. This result extends to approximately sparse vectors x. Our result is universal in the sense that with high probability, one measurement scheme will successfully recover all sparse vectors simultaneously. The argument is based on solving an equivalent geometric problem on random hyperplane tessellations.
“Seedling” Mesenchymal Tumors (Gastrointestinal Stromal Tumors and Leiomyomas) are Common Incidental Tumors of the Esophagogastric Junction

Gastrointestinal stromal tumors (GISTs) are the most common nonepithelial neoplasm of the gastrointestinal tract and show a predilection for the stomach. Most are detected because of symptoms, but some are incidental findings at autopsy or surgery for other reasons. Incidental GISTs tend to be smaller at diagnosis, but even small (<1 cm) GISTs have been shown to harbor activating KIT mutations at rates similar to advanced GISTs. However, the prevalence and characteristics of small GISTs in surgical resections of the esophagogastric junction (EGJ) remains unclear. We studied 150 esophagogastric resections for esophageal or EGJ carcinomas (100 with preoperative chemoradiation and 50 untreated cases) that had been extensively embedded for histologic examination (mean 30 sections/case). Number, size, morphology, and location of all GISTs and leiomyomas were recorded. All potential GISTs were evaluated with CD117 and CD34 immunohistochemistry, and a subset (35) leiomyomas with smooth muscle actin, desmin, and CD117. We found 18 incidental GISTs in 15 of 150 (10%) patients; 3 patients harbored 2 separate lesions. Prevalence of GIST was identical in treated (10 of 100) and untreated (5 of 50) cases. All (100%) showed positivity for both CD117 and CD34 and all were of spindle cell morphology. Lesions ranged from 0.2 to 3.0 mm in size (mean 1.3 mm). Eight (44%) were based in the outer muscularis propria, 7 (39%) in inner muscularis, and 3 (17%) between the muscle layers. The lesions tended to cluster near the EGJ, with 8 (44%) on the gastric side, 9 (50%) on the esophageal side, and 1 (6%) undetermined owing to overlying ulceration. Leiomyomas were even more common than GIST, occurring in 47% of patients (44% of treated and 52% of untreated, P=0.39), with a mean of 3 leiomyomas per patient (range 1 to 13) and mean size of 1.7 mm (range 0.2 to 12 mm). Unlike colorectal leiomyomas, most (91%) EGJ leiomyomas were located in the inner muscularis propria and only rarely (1%) in muscularis mucosa. These results suggest that GIST and leiomyoma are common incidental “seedling” lesions of the EGJ, found in 10% and 47% of patients undergoing surgery for esophageal carcinoma. The common occurrence of microscopic GISTs compared with the rarity of clinically manifest and malignant esophagogastric GISTs suggests that additional genetic or epigenetic alterations must happen for neoplastic progression.
Disrupting Circadian Homeostasis of Sympathetic Signaling Promotes Tumor Development in Mice

Background Cell proliferation in all rapidly renewing mammalian tissues follows a circadian rhythm that is often disrupted in advanced-stage tumors. Epidemiologic studies have revealed a clear link between disruption of circadian rhythms and cancer development in humans. Mice lacking the circadian genes Period1 and 2 (Per) or Cryptochrome1 and 2 (Cry) are deficient in cell cycle regulation and Per2 mutant mice are cancer-prone. However, it remains unclear how circadian rhythm in cell proliferation is generated in vivo and why disruption of circadian rhythm may lead to tumorigenesis. Methodology/Principal Findings Mice lacking Per1 and 2, Cry1 and 2, or one copy of Bmal1, all show increased spontaneous and radiation-induced tumor development. The neoplastic growth of Per-mutant somatic cells is not controlled cell-autonomously but is dependent upon extracellular mitogenic signals. Among the circadian output pathways, the rhythmic sympathetic signaling plays a key role in the central-peripheral timing mechanism that simultaneously activates the cell cycle clock via AP1-controlled Myc induction and p53 via peripheral clock-controlled ATM activation. Jet-lag promptly desynchronizes the central clock-SNS-peripheral clock axis, abolishes the peripheral clock-dependent ATM activation, and activates myc oncogenic potential, leading to tumor development in the same organ systems in wild-type and circadian gene-mutant mice. Conclusions/Significance Tumor suppression in vivo is a clock-controlled physiological function. The central circadian clock paces extracellular mitogenic signals that drive peripheral clock-controlled expression of key cell cycle and tumor suppressor genes to generate a circadian rhythm in cell proliferation. Frequent disruption of circadian rhythm is an important tumor promoting factor.
Instability criteria for Lur'e systems toward oscillation analysis of uncertain gene networks

In this paper, we derive some instability criteria for Lur'e -type nonlinear systems. First, we define absolute instability. Then, linear matrix inequality conditions for absolute instability are derived. The obtained conditions are analogous to well-known circle-type and Popov-type stability criteria. Finally, we evaluate the usefulness through an application to instability analysis of an uncertain genetic network model.
Nonalcoholic Fatty Liver Disease Is Associated with Aortic Valve Sclerosis in Patients with Type 2 Diabetes Mellitus

Background Recent epidemiological data suggest that non-alcoholic fatty liver disease (NAFLD) is closely associated with aortic valve sclerosis (AVS), an emerging risk factor for adverse cardiovascular outcomes, in nondiabetic and type 2 diabetic individuals. To date, nobody has investigated the association between NAFLD and AVS in people with type 2 diabetes, a group of individuals in which the prevalence of these two diseases is high. Methods and Results We recruited 180 consecutive type 2 diabetic patients without ischemic heart disease, valvular heart disease, hepatic diseases or excessive alcohol consumption. NAFLD was diagnosed by liver ultrasonography whereas AVS was determined by conventional echocardiography in all participants. In the whole sample, 120 (66.7%) patients had NAFLD and 53 (29.4%) had AVS. No patients had aortic stenosis. NAFLD was strongly associated with an increased risk of prevalent AVS (odds ratio [OR] 2.79, 95% CI 1.3–6.1, p<0.01). Adjustments for age, sex, duration of diabetes, diabetes treatment, body mass index, smoking, alcohol consumption, hypertension, dyslipidemia, hemoglobin A1c and estimated glomerular filtration rate did not attenuate the strong association between NAFLD and risk of prevalent AVS (adjusted-OR 3.04, 95% CI 1.3–7.3, p = 0.01). Conclusions Our results provide the first demonstration of a positive and independent association between NAFLD and AVS in patients with type 2 diabetes mellitus.
Gaussian Process Approach to Remote Sensing Image Classification

Gaussian processes (GPs) represent a powerful and interesting theoretical framework for Bayesian classification. Despite having gained prominence in recent years, they remain an approach whose potentialities are not yet sufficiently known. In this paper, we propose a thorough investigation of the GP approach for classifying multisource and hyperspectral remote sensing images. To this end, we explore two analytical approximation methods for GP classification, namely, the Laplace and expectation-propagation methods, which are implemented with two different covariance functions, i.e., the squared exponential and neural-network covariance functions. Moreover, we analyze how the computational burden of GP classifiers (GPCs) can be drastically reduced without significant losses in terms of discrimination power through a fast sparse-approximation method like the informative vector machine. Experiments were designed aiming also at testing the sensitivity of GPCs to the number of training samples and to the curse of dimensionality. In general, the obtained classification results show clearly that the GPC can compete seriously with the state-of-the-art support vector machine classifier.
Treatment trends for retinopathy of prematurity in the UK: active surveillance study of infants at risk

Objectives To estimate the incidence of severe retinopathy of prematurity (ROP) requiring treatment and describe current treatment patterns in the UK. Design Nationwide population-based case ascertainment study via the British Ophthalmic Surveillance Unit and a national collaborative ROP special interest group. Practitioners completed a standardised case report form (CRF). Setting All paediatric ophthalmologists providing screening and/or treatment for retinopathy in the UK were invited to take part. Participants Any baby with ROP treated or referred for treatment between 1 December 2013 and 30 November 2014, treated with laser, cryotherapy, vascular endothelial growth factor (VEGF) inhibitor or vitrectomy/scleral buckling, or a combination. Main outcome measure Incidence of ROP requiring treatment. Results We received 370 CRFs; 327 were included. Denominator from epidemiological data: 8112 infants with birth weight of <1500 g. The incidence of ROP requiring treatment was 4% (327/8112, 95% CI 3.6% to 4.5%). Median gestational age was 25 weeks (IQR 24.3–26.1), and median birth weight 706 g (IQR 620–821). Median age at first treatment was 80 days (IQR 71–96). 204 right eyes (62.39%) had type 1 ROP, and 27 (8.26%) had aggressive posterior ROP. Infants were also treated for milder disease: 9 (2.75%) right eyes were treated for type 2 ROP, and 74 (22.63%) for disease milder than type 1 with plus or preplus, which we defined here as ‘type 2 plus’ disease. First-line treatment was diode laser photoablation of the avascular retina in 90.5% and injection of VEGF inhibitor in 8%. Conclusions ROP treatment incidence in the UK is 2.5 times higher than previously estimated. 8% of treated infants receive intravitreal VEGF inhibitor, currently unlicensed. Research is needed urgently to establish safety and efficacy of this approach. Earlier treatment and increasing numbers of surviving premature infants require an increase in appropriate eye care facilities and staff. Trial registration number NCT02484989.
False Belief vs. False Photographs: A Test of Theory of Mind or Working Memory?

Theory of mind (ToM), the ability to reason about other people’s thoughts and beliefs, has been traditionally studied in behavioral and neuroimaging experiments by comparing performance in “false belief” and “false photograph” (control) stories. However, some evidence suggests that these stories are not matched in difficulty, complicating the interpretation of results. Here, we more fully evaluated the relative difficulty of comprehending these stories and drawing inferences from them. Subjects read false belief and false photograph stories followed by comprehension questions that probed true (“reality” questions) or false beliefs (“representation” questions) appropriate to the stories. Stories and comprehension questions were read and answered, respectively, more slowly in the false photograph than false belief conditions, indicating their greater difficulty. Interestingly, accuracy on representation questions for false photograph stories was significantly lower than for all other conditions and correlated positively with participants’ working memory span scores. These results suggest that drawing representational inferences from false photo stories is particularly difficult and places heavy demands on working memory. Extensive naturalistic practice with ToM reasoning may enable a more flexible and efficient mental representation of false belief stories, resulting in lower memory load requirements. An important implication of these results is that the differential modulation of right temporal–parietal junction (RTPJ) during ToM and “false photo” control conditions may reflect the documented negative correlation of RTPJ activity with working memory load rather than a specialized involvement in ToM processes.
Creation of Stable Heterothallic Strains of Komagataella phaffii Enables Dissection of Mating Gene Regulation

ABSTRACT The methylotrophic yeast Komagataella phaffii (Pichia pastoris) is homothallic and has been reported to switch mating type by an ancient inversion mechanism. Two mating-type (MAT) loci include homologs of the MATa and MATα transcription factor genes, with the expression from one locus downregulated by telomere position effects. However, not much is known about mating gene regulation, since the mixture of mating types complicates detailed investigations. In this study, we developed K. phaffii strains with stable mating types by deletion of the inverted-repeat region required for mating-type switching. These heterothallic strains retain their ability to mate with cells of the opposite mating type and were used to further elucidate mating gene regulation. Functional analysis of MAT mutant strains revealed the essential role of MATa2 and MATα1 in diploid cell formation. Disruption of MATa1 or MATα2 did not affect mating; however, in diploid cells, both genes are required for sporulation and the repression of shmoo formation. The heterothallic strains generated in this study allowed the first detailed characterization of mating gene regulation in K. phaffii. They will be a valuable tool for further studies investigating cell-type-specific behavior and will enable in-depth genetic analyses and strain hybridization in this industrially relevant yeast species.
The Contents and Readability of Informed Consent Forms for Oncology Clinical Trials

Objectives:To compare the quality of informed consent forms (ICF) for different trial phases, funding sources, oncology subspecialties, disease settings, and intervention modalities. Methods:ICF for prospectively conducted clinical trials were examined for their descriptions of benefits and risks, study alternatives, voluntary participation, and confidentiality. Readability was assessed with Flesch Reading Ease (FRE) score and Flesch-Kincaid Reading Grade Level. Results:Among 262 evaluable trials, ICF contained an average of 3982 words, 379 sentences, and 10.5 pages. The mean FRE score and Reading Grade Level were 61.2 and 7.4, respectively. All ICF explicitly stated that the intervention was investigational. Only 2 (1%) promised direct personal benefits, 16 (6%) suggested the chance of cure or prolonged survival, and 89 (34%) indicated a potential for tumor response. Conversely, 239 (91%) mentioned the risk of serious harms, 217 (83%) admitted that some side effects could be unknown or unpredictable, and 126 (48%) reported hospitalization or death as a possibility. Alternatives to participation, right to withdraw from study, and data confidentiality were addressed in 242 (92%), 254 (97%), and 260 (99%) ICF, respectively. Hematology, industry-funded, metastatic, and systemic therapy trials were most likely to highlight major risks (P < 0.05). Readability was better in phase I trials and in studies, which were performed by medical oncologists, sponsored by governmental agencies, conducted in the metastatic setting, and involved systemic therapy (P < 0.05). Conclusions:ICF had acceptable readability and provided a realistic overview of the benefits and risks of clinical trials, but the potential for hospitalization or fatality was underreported.
Visual Entropy Metric Reveals Differences in Drivers' Eye Gaze Complexity across Variations in Age and Subsidiary Task Load

The purpose of this study was to evaluate the global complexity of drivers' eye movement behavior as a function of advanced adult age and variations in information processing resource demands. Global complexity was operationalized using an information theory metric commonly known as entropy. Fourteen young (mean age = 27) and 14 older (mean age = 75) participants drove on a 2-lane rural highway while simultaneously performing a subsidiary loading task designed to increase cognitive demands drawing upon either verbal-memory resources or visual-spatial resources (within the context of Wickens' (1980) multiple resource model of attention). Compared to traditional distributional measures of eye movement behavior such as mean saccade amplitude and fixation dwell time, the entropy measure of global complexity was better able to distinguish between young and old drivers as well as between baseline driving and conditions of high visual-spatial task load. These results strongly suggest that global measures of eye movement behavior hold significant potential for increasing our understanding of the interacting effects of normal adult aging and task-induced cognitive demands within the context of real-world driving.
Improved scFv Anti-LOX-1 Binding Activity by Fusion with LOX-1-Binding Peptides

The oxidized low-density lipoprotein receptor-1 (LOX-1) targeted single-chain variable fragment (scFvs) is a promising molecule for the targeted delivery of imaging and therapeutic molecules of atherosclerotic diseases; however, its applications are limited by the inherent low antigen affinity. In this study, the three-dimensional (3D) model of the anti-LOX-1 scFv was constructed and its docking with the LOX-1 protein was developed. To improve the LOX-1-binding activity, the anti-LOX-1 scFv was designed to fuse with one of three LOX-1-binding heptapeptides, LTPATAI, FQTPPQL, and LSIPPKA, at its N-terminus and C-terminus and in the linker region, which have different LOX-1-binding interfaces with the anti-LOX-1 scFv analyzed by an array of computational approaches. These scFv/peptide fusions were constructed, successfully expressed in Brevibacillus choshinensis hosts, and purified by a two-step column purification process. The antigen binding activity, structural characteristics, thermal stability, and stability in serum of these fusion proteins were examined. Results showed that the scFv with N-terminal fusing peptides proteins demonstrated increased LOX-1-binding activity without decrease in stability. These findings will help increase the application efficacy of LOX-1 targeting scFv in LOX-1-based therapy.
Electrophysiology of the sodium-potassium-ATPase in cardiac cells.

Like several other ion transporters, the Na(+)-K(+) pump of animal cells is electrogenic. The pump generates the pump current I(p). Under physiological conditions, I(p) is an outward current. It can be measured by electrophysiological methods. These methods permit the study of characteristics of the Na(+)-K(+) pump in its physiological environment, i.e., in the cell membrane. The cell membrane, across which a potential gradient exists, separates the cytosol and extracellular medium, which have distinctly different ionic compositions. The introduction of the patch-clamp techniques and the enzymatic isolation of cells have facilitated the investigation of I(p) in single cardiac myocytes. This review summarizes and discusses the results obtained from I(p) measurements in isolated cardiac cells. These results offer new exciting insights into the voltage and ionic dependence of the Na(+)-K(+) pump activity, its effect on membrane potential, and its modulation by hormones, transmitters, and drugs. They are fundamental for our current understanding of Na(+)-K(+) pumping in electrically excitable cells.
Combined FT-Raman and SEM studies of the effects of Er:YAG laser irradiation on dentin.

OBJECTIVE This study evaluated the molecular and morphological changes on dentin elements after Er:YAG laser irradiation. BACKGROUND DATA Spectroscopy studies reporting the effects of Er:YAG laser irradiation as an alternative to acid etching are needed to better understand the laser's effects. METHODS The occlusal one-third of the crown of six human third molars was removed. The dentin surface was schematically divided into areas corresponding to four surface treatment groups: control (group C): 37% phosphoric acid etching; group I: Er:YAG laser 80 mJ; group II: Er:YAG laser 120 mJ; and group III: Er:YAG laser 180 mJ. The analysis was performed by scanning electron microscopy (SEM) and Fourier transform Raman spectroscopy (FT-Raman) before and after the treatments. Raman data were submitted to ANOVA and Bonferroni tests. RESULTS The SEM photomicrographs revealed open dentin tubules in the control group. The molars from groups I, II, and III showed partially open dentin tubules. SEM images showed that the laser-irradiated dentin surface was not favorable to the diffusion of monomers. A significant reduction of the spectra relative intensity was observed in group III specimens. CONCLUSIONS Er:YAG laser irradiation with 180 mJ could produce chemical changes in proteins, phosphate, and carbonate in dentin.
A low cost instrumentation system for determining stability of dental implants

A low cost instrumentation system has been proposed in this paper to determine the stability of dental implants. For this purpose, Resonance Frequency Analysis technique has been used to monitor the changes in resonance frequency that takes place during the bonding of the dental implant with the surrounding bones and tissues [1]. In the present work, the designed instrumentation system has been characterized and its performance validated in in-vitro experiments. From this study, it is observed that the instrumentation system developed can be used for determining stability of dental implants. There is, however, scope for improvements in terms of the resolution and the real-time performance of the system.
Prevalence of distal colonic neoplasia associated with proximal colon cancers.

BACKGROUND The number, size, and histologic features of distal colorectal adenomatous polyps have been reported to correlate with the risk of developing proximal colon cancer. To investigate this putative relationship further, we evaluated the frequency of distal colorectal neoplastic polyps in patients with colon cancer located proximal to the splenic flexure. METHODS All cases of colorectal adenocarcinomas treated at a tertiary referral center and Veterans Affairs hospital between 1979 and 1992 were identified by International Classification of Diseases coding and review of pathology and colonoscopy reports. The medical records of patients with documented cancers proximal to the splenic flexure were examined for the presence, location, size, and histopathologic features of synchronous neoplastic lesions found at colonoscopy. RESULTS Among 634 patients with colorectal cancer identifiable by location, 172 had proximally located tumors. Of these, 60 patients were excluded because of lack of complete colonoscopy or because surgical resection was performed elsewhere. Forty percent of the remaining 112 patients for whom data could be evaluated demonstrated neoplastic lesions in addition to the proximal cancer. The colon was devoid of "sentinel" neoplasia distal to the splenic flexure and descending colon-sigmoid colon junction in 69% and 72% of patients, respectively. CONCLUSIONS The majority of proximal colon cancers are not associated with distal sentinel lesions. We surmise that flexible sigmoidoscopy will fail to find evidence of neoplasia in at least 25% of patients with prevalent colon cancers.