Miracle-dz/UniFAR-FTUs huggingface dataset:
Featherweight OCL: A Proposal for a Machine-Checked Formal Semantics for OCL 2.5

The Unified Modeling Language (UML) is one of the few modeling languages that is widely used in industry. While UML is mostly known as diagrammatic modeling language (e.g., visualizing class models), it is complemented by a textual language, called Object Constraint Language (OCL). OCL is a textual annotation language, originally based on a three-valued logic, that turns UML into a formal language. Unfortunately the semantics of this specification language, captured in the "Annex A" of the OCL standard, leads to different interpretations of corner cases. Many of these corner cases had been subject to formal analysis since more than ten years.The situation complicated with the arrival of version 2.3 of the OCL standard. OCL was aligned with the latest version of UML: this led to the extension of the three-valued logic by a second exception element, called null. While the first exception element invalid has a strict semantics, null has a non strict interpretation. The combination of these semantic features lead to remarkable confusion for implementors of OCL compilers and interpreters.In this paper, we provide a formalization of the core of OCL in HOL. It provides denotational definitions, a logical calculus and operational rules that allow for the execution of OCL expressions by a mixture of term rewriting and code compilation. Moreover, we describe a coding-scheme for UML class models that were annotated by code-invariants and code contracts. An implementation of this coding-scheme has been undertaken: it consists of a kind of compiler that takes a UML class model and translates it into a family of definitions and derived theorems over them capturing the properties of constructors and selectors, tests and casts resulting from the class model. However, this compiler is not included in this document.Our formalization reveals several inconsistencies and contradictions in the current version of the OCL standard. They reflect a challenge to define and implement OCL tools in a uniform manner. Overall, this document is intended to provide the basis for a machine-checked text "Annex A" of the OCL standard targeting at tool implementors.
Factors that distinguish college students with depressive symptoms with and without suicidal thoughts.

BACKGROUND Suicide among college students is a significant public health concern. Although suicidality is linked to depression, not all depressed college students experience suicidal ideation (SI). The primary aim of this study was to determine potential factors that may distinguish college students with depressive symptoms with and without SI. METHODS A total of 287 undergraduate college students with substantial depressive symptoms (Beck Depression Inventory [BDI] total score >13) with and without SI were compared across psychiatric and functional outcome variables. Independent sample t tests were conducted for each outcome variable using the suicide item of the BDI as a dichotomous (ie, zero vs nonzero score) grouping variable. RESULTS Relative to students with substantial depressive symptoms without SI, those with SI were more symptomatic overall, having significantly higher levels of depressive symptoms, hopelessness, and anxiety. However, contrary to our expectations, nonsuicidal and suicidal students did not differ on measures of everyday functioning (ie, cognitive and physical functioning and grade point average). CONCLUSIONS Our findings suggest that SI among college students is associated with increased subjective distress but may not adversely impact physical or cognitive functioning or academic performance.
Measuring and Representing the Performance of Manufacturing Assembly Robots

With the growth of robotic technology, there is a need for performance measures to characterize and compare robots and to help determine which features are most suited to a particular application. Robot systems are complex and involve a wide range of features and performance characteristics whose importance differs depending on the application domain. This paper describes a set of assembly performance measures associated with the different features along with an exploration of how one could represent this information. It organizes the assembly measures in reference to a taxonomy of assembly skills and tasks. Arranging the performance measures in this way will simplify the task of selecting a particular robot system for an assembly task by helping focus on those aspects of the task that are most critical.
Heterogeneous Effects of Direct Hypoxia Pathway Activation in Kidney Cancer

General activation of hypoxia-inducible factor (HIF) pathways is classically associated with adverse prognosis in cancer and has been proposed to contribute to oncogenic drive. In clear cell renal carcinoma (CCRC) HIF pathways are upregulated by inactivation of the von-Hippel-Lindau tumor suppressor. However HIF-1α and HIF-2α have contrasting effects on experimental tumor progression. To better understand this paradox we examined pan-genomic patterns of HIF DNA binding and associated gene expression in response to manipulation of HIF-1α and HIF-2α and related the findings to CCRC prognosis. Our findings reveal distinct pan-genomic organization of canonical and non-canonical HIF isoform-specific DNA binding at thousands of sites. Overall associations were observed between HIF-1α-specific binding, and genes associated with favorable prognosis and between HIF-2α-specific binding and adverse prognosis. However within each isoform-specific set, individual gene associations were heterogeneous in sign and magnitude, suggesting that activation of each HIF-α isoform contributes a highly complex mix of pro- and anti-tumorigenic effects.
Two-photon polymerization of polyethylene glycol diacrylate scaffolds with riboflavin and triethanolamine used as a water-soluble photoinitiator.

AIM In this study, the suitability of a mixture containing riboflavin (vitamin B2) and triethanolamine (TEOHA) as a novel biocompatible photoinitiator for two-photon polymerization (2PP) processing was investigated. MATERIALS & METHODS Polyethylene glycol diacrylate was crosslinked using Irgacure(®) 369, Irgacure 2959 or a riboflavin-TEOHA mixture; biocompatibility of the photopolymer extract solutions was subsequently assessed via endothelial cell proliferation assay, endothelial cell viability assay and single-cell gel electrophoresis (comet) assay. Use of a riboflavin-TEOHA mixture as a photoinitiator for 2PP processing of a tissue engineering scaffold and subsequent seeding of this scaffold with GM-7373 bovine aortic endothelial cells was also demonstrated. RESULTS The riboflavin-TEOHA mixture was found to produce much more biocompatible scaffolds than those produced with Irgacure 369 or Irgacure 2959. CONCLUSION The results suggest that riboflavin is a promising component of photoinitiators for 2PP fabrication of tissue engineering scaffolds and other medically relevant structures (e.g., biomicroelectromechanical systems).
Design and Calibration of a Specialized Polydioptric Camera Rig

It has been observed in the nature that all creatures have evolved highly exclusive sensory organs depending on their habitat and the form of resources availability for their survival. In this project, a novel omnidirectional camera rig, inspired from natural vision sensors, is proposed. It is exclusively designed to operate for highly specified tasks in the field of mobile robotics. Navigation problems on uneven terrains and detection of the moving objects while the robot is itself in motion are the core problems that omnidirectional systems tackle. The proposed omnidirectional system is a compact and a rigid vision system with dioptric cameras that provide a 360 degrees field-of-view in horizontal and vertical, with no blind spot in their site combined with a high-resolution stereo camera to monitor anterior field-of-view for a more accurate perception with depth information of the scene. Structure-from-motion algorithm is adapted and implemented to prove the design validity of the proposed camera rig and a toolbox is developed to calibrate similar systems.
State dependent parametrizations for nonlinear MPC

Abstract This paper aims at reducing the computational load caused by the online optimization in nonlinear model predictive control (MPC) by introducing a new type of parametrizations for the predicted input trajectory. In order to determine offline the state dependent parametrizations, a tailored data mining algorithm is introduced. Refinements to achieve feasibility of the parametrized constrained optimization problem are presented. Theoretical guarantees on constraint satisfaction and feasibility employing the parametrizations are provided for Lipschitz continuous systems. In a numerical example the benefits of the new method are illustrated.
Metabolic Engineering of Seeds Can Achieve Levels of ω-7 Fatty Acids Comparable with the Highest Levels Found in Natural Plant Sources1[OA]

Plant oils containing ω-7 fatty acids (FAs; palmitoleic 16:1Δ9 and cis-vaccenic 18:1Δ11) have potential as sustainable feedstocks for producing industrially important octene via metathesis chemistry. Engineering plants to produce seeds that accumulate high levels of any unusual FA has been an elusive goal. We achieved high levels of ω-7 FA accumulation by systematic metabolic engineering of Arabidopsis (Arabidopsis thaliana). A plastidial 16:0-ACP desaturase has been engineered to convert 16:0 to 16:1Δ9 with specificity >100-fold than that of naturally occurring paralogs, such as that from cat's claw vine (Doxantha unguis-cati). Expressing this engineered enzyme (Com25) in seeds increased ω-7 FA accumulation from <2% to 14%. Reducing competition for 16:0-ACP by down-regulating the β-ketoacyl-ACP synthase II 16:0 elongase further increased accumulation of ω-7 FA to 56%. The level of 16:0 exiting the plastid without desaturation also increased to 21%. Coexpression of a pair of fungal 16:0 desaturases in the cytosol reduced the 16:0 level to 11% and increased ω-7 FA to as much as 71%, equivalent to levels found in Doxantha seeds.
GPIHBP1: an endothelial cell molecule important for the lipolytic processing of chylomicrons

Purpose of review To summarize recent data indicating that glycosylphosphatidylinositol-anchored high density lipoprotein-binding protein 1 (GPIHBP1) plays a key role in the lipolytic processing of chylomicrons. Recent findings Lipoprotein lipase hydrolyses triglycerides in chylomicrons at the luminal surface of the capillaries in heart, adipose tissue, and skeletal muscle. The endothelial cell molecule that facilitates the lipolytic processing of chylomicrons has never been clearly defined. Mice lacking GPIHBP1 manifest chylomicronemia, with plasma triglyceride levels as high as 5000 mg/dl. In wild-type mice, GPIHBP1 is expressed on the luminal surface of capillaries in heart, adipose tissue, and skeletal muscle. Cells transfected with GPIHBP1 bind both chylomicrons and lipoprotein lipase avidly. Summary The chylomicronemia in Gpihbp1-deficient mice, the fact that GPIHBP1 is located within the lumen of capillaries, and the fact that GPIHBP1 binds lipoprotein lipase and chylomicrons suggest that GPIHBP1 is a key platform for the lipolytic processing of triglyceride-rich lipoproteins.
An Augmented Reality-Assisted Therapeutic Healthcare Exercise System Based on Bare-Hand Interaction

ABSTRACT Augmented Reality (AR)-assisted exercises for the enhancement of finger functions have been developed for many years and have proven to be effective. Most applications tracked the motion of upper-extremity using handheld trackers, which are not convenient to put on and take off. Bare-hand tracking algorithms have been utilized to address this limitation; however, only few AR-assisted healthcare approaches have been designed to train upper-extremity skills using bare-hand tracking, and even fewer approaches detect the Range of Motion (ROM) of fingers with low-cost devices. This paper presents a low-cost and multi-modal residential-based AR-assisted therapeutic healthcare exercise system. A computer vision-based bare-hand interaction method is proposed in this system. This method is designed to estimate finger bending degrees through their projection lengths. With an accurate feature detection strategy, this method is able to detect the full ROM using two web cameras. This system also incorporates a vibration wrist band to stimulate the users with tactile feedback, and an assessment module to evaluate user performance.
The Mediating Effect of Psychosocial Factors on Suicidal Probability among Adolescents

Suicidal probability is an actual tendency including negative self-evaluation, hopelessness, suicidal ideation, and hostility. The purpose of this study was to examine the role of psychosocial variances in the suicidal probability of adolescents, especially the role of mediating variance. This study investigated the mediating effects of psychosocial factors such as depression, anxiety, self-esteem, stress, and social support on the suicidal probability among 1,586 adolescents attending middle and high schools in the Kyunggi Province area of South Korea. The relationship between depression and anxiety/suicidal probability was mediated by both social resources and self-esteem. Furthermore, the influence of social resources was mediated by interpersonal and achievement stress as well as self-esteem. This study suggests that suicidal probability in adolescents has various relationships, including mediating relations, with several psychosocial factors. The interventions on suicidal probability in adolescents should focus on social factors as well as clinical symptoms.
Model-based detection of lung nodules in computed tomography exams. Thoracic computer-aided diagnosis.

RATIONALE AND OBJECTIVES In this study, we developed a prototype model-based computer aided detection (CAD) system designed to automatically detect both solid and subsolid pulmonary nodules in computed tomography (CT) images. By using this CAD algorithm, along with the radiologist's initial interpretation, we aim to improve the sensitivity of radiologic readings of CT lung exams. MATERIALS AND METHODS We have developed a model-based CAD algorithm through the use of precise mathematic models that capture scanner physics and anatomic information. Our model-based CAD algorithm uses multiple segmentation algorithms to extract noteworthy structures in the lungs and a Bayesian statistical model selection framework to determine the probability of various anatomical events throughout the lung. We tested this algorithm on 50 low-dose CT lung cancer screening cases in which ground truth was produced through readings by three expert chest radiologists. RESULTS Using this model-based CAD algorithm on 50 low-dose CT cases, we measured potential sensitivity improvements of 7% and 5% in two radiologists with respect to all noncalcified nodules, solid and subsolid, greater than 5 mm in diameter. The third radiologist did not miss any nodules in the ground truth set. The CAD algorithm produced 8.3 false positives per case. CONCLUSION Our prototype CAD system demonstrates promising results as a tool to improve the quality of radiologic readings by increasing radiologist sensitivity. A significant advantage of this model-based approach is that it can be easily extended to support additional anatomic models as clinical understanding and scanning practices improve.
A generalized Gilbert-Varshamov bound derived via analysis of a code-search algorithm

A generalization of the Gilbert-Varshamov bound that is applicable to block codes whose codewords must be drawn from irregular sets is derived. The bound improves by a factor of four a similar result derived by V.D. Kolesnik and V.Y. Krachkovsky (1991). This generalization is derived by analysing a code search algorithm referred to as the altruistic algorithm. This algorithm iteratively deletes potential codewords so that at each iteration the candidate is removed. The bound is derived by demonstrating that, as the algorithm proceeds, the average volume of a sphere of a given radius approaches the maximum such volume and so a bound previously expressed in terms of the maximum volume can in fact be expressed in terms of the average volume. Examples of applications where the bound is relevant include error-correcting (d,k) codes and binary codes for code division multiple access. >
CDK9/cyclin complexes modulate endoderm induction by direct interaction with Mix.3/mixer

Mix‐related homeodomain proteins are involved in endoderm formation in the early vertebrate embryo. We used a yeast two‐hybrid screen to identify proteins that interact with Mix.3/mixer to regulate endoderm induction. We demonstrate that cyclin‐dependent kinase 9 (CDK9) interacts with the carboxyl terminal domain of Mix.3. CDK9 is the catalytic subunit of the PTEF‐b transcription elongation complex that phosphorylates the C‐terminal domain of RNA polymerase II to promote efficient elongation of nascent transcripts. Using whole embryo transcription reporter and animal pole explant assays, we show that Mix.3 activity is regulated by CDK9/cyclin complexes. Co‐expression of cyclin T2 and cyclin K had different effects on Mix.3 transcriptional activity and endoderm induction. Our data suggest that binding of CDK9, and the recruitment of different cyclin partners, can modulate the endoderm‐inducing activity of Mix.3 during embryonic development. Developmental Dynamics 238:1346–1357, 2009. © 2009 Wiley‐Liss, Inc.
A Phase I study with an anti-CD30 ricin A-chain immunotoxin (Ki-4.dgA) in patients with refractory CD30+ Hodgkin's and non-Hodgkin's lymphoma.

Ki-4.dgA is an anti-CD30 immunotoxin (IT) constructed by coupling the monoclonal antibody Ki-4 via a sterically hindered disulfide linker to deglycosylated ricin A-chain. This IT was efficacious in vitro and in SCID mice with disseminated human Hodgkin's lymphoma. Accordingly, a Phase I trial in patients (pts) with Hodgkin's lymphoma was designed. The objectives of this Phase I trial were to determine the maximum tolerated dose, the dose-limiting toxicities, pharmacokinetics, and antitumor activity. Seventeen pts with relapsed CD30+ lymphoma were treated with escalating doses (5, 7.5, or 10 mg/m(2)/cycle) of the IT as four bolus infusions on days 1, 3, 5, and 7 for one to three cycles. All of the pts had progressive disease and were heavily pretreated. Nine had primary progressive disease and 14 had advanced disease with massive tumor burdens. The mean age was 35 years (24-52 years). Peak serum concentrations of the intact IT varied from 0.23 to 1.1 microg/ml. Side effects and dose-limiting toxicities were related to vascular leak syndrome, i.e., decreases in serum albumin, edema, weight gain, hypotension, tachycardia, myalgia, and weakness. The maximum tolerated dose was 5 mg/m(2). Seven of 17 (40%) pts made human antiricin antibodies (> or =1.0 microg/ml), and 1 pt developed human antimouse antibodies (> or =1.0 microg/ml). Clinical response in the 15 evaluable pts included 1 partial remission, 1 minor response, and 2 stable diseases. In conclusion, the IT was less well tolerated than other ITs of this type. This might be because of the low number of CD30+ peripheral blood mononuclear cells, and in part because of binding of the IT to soluble CD30 antigen and the resulting circulation of IT/sCD30 complexes.
Evaluating the consistency of estimation

The error covariance reported by an estimation is said to be consistent if it is a reliable indicator of the actual error. In this paper several types of consistency are defined, and methods for its evaluation are introduced. Mean Squared Deviation consistency is based on the Chebyshev inequality, p equivalence is based on the fact that the concentration ellipse with probability mass p must contain the actual value of the estimated parameter with probability p, and Normalized Deviation Squared (NDS) consistency implies that a concentration ellipse of probability mass p contains the actual value of the estimated parameter with probability at least p. Hypothesis tests for consistency evaluation are presented. The NDS consistency test is applied to WiFi localization system data in order to investigate sources of inconsistencies and adjust parameters of the system. It is shown that underestimated measurement noise is the main cause of inconsistent behavior; however, an incorrect motion model or underestimated process noise might also result in inconsistent estimates.
Lung cancer in a nonsmoking underground uranium miner.

Working in mines is associated with acute and chronic occupational disorders. Most of the uranium mining in the United States took place in the Four Corners region of the Southwest (Arizona, Colorado, New Mexico, and Utah) and on Native American lands. Although the uranium industry collapsed in the late 1980s, the industry employed several thousand individuals who continue to be at increased risk for developing lung cancers. We present the case of a 72-year-old Navajo male who worked for 17 years as an underground uranium miner and who developed lung cancer 22 years after leaving the industry. His total occupational exposure to radon progeny was estimated at 506 working level months. The miner was a life-long nonsmoker and had no other significant occupational or environmental exposures. On the chest X-ray taken at admission into the hospital, a right lower lung zone infiltrate was detected. The patient was treated for community-acquired pneumonia and developed respiratory failure requiring mechanical ventilation. Respiratory failure worsened and the patient died 19 days after presenting. On autopsy, a 2.5 cm squamous cell carcinoma of the right lung arising from the lower lobe bronchus, a right broncho-esophageal fistula, and a right lower lung abscess were found. Malignant respiratory disease in uranium miners may be from several occupational exposures; for example, radon decay products, silica, and possibly diesel exhaust are respiratory carcinogens that were commonly encountered. In response to a growing number of affected uranium miners, the Radiation Exposure Compensation Act (RECA) was passed by the U.S. Congress in 1990 to make partial restitution to individuals harmed by radiation exposure resulting from underground uranium mining and above-ground nuclear tests in Nevada.