Miracle-dz/UniFAR-FTUs huggingface dataset:
Mechanical verification of refactorings

In this paper we describe the formal verification of refactorings for untyped and typed lambda-calculi. This verification is performed in the proof assistant Isabelle/HOL. Refactorings are program transformations applied to improve the design of source code. Well-structured source code is easier and cheaper to maintain, and this motivates the use of refactoring. These transformations have been implemented as programmer tools and, as with other metaprogramming tools, it is desirable that implementations of refactorings are correct. For a refactoring to be correct the refactored program must be identical in behaviour to the original program. Since refactorings are source-to-source transformations, concrete program information matters: for example, names (of variables, procedures, etc) and program layout should also be preserved by refactoring. This is a particular characteristic of refactorings since general program transformations operate over machine representations of programs, rather than readable source code. The paper describes the formalisation adopted, and the alternatives explored. It also reflects on some of the difficulties of performing such formalisations, the interaction between refactoring and phases such as type-checking and parsing, and the generation of correctimplementations from mechanised proofs.
A G1127S Change in Calcium-binding Epidermal Growth Factor-like Domain 13 of Human Fibrillin-1 Causes Short Range Conformational Effects*

Human fibrillin-1, an extracellular matrix glycoprotein, has a modular organization that includes 43 calcium-binding epidermal growth factor-like (cbEGF) domains arranged as multiple tandem repeats. A missense mutation that changes a highly conserved glycine to serine (G1127S) has been identified in cbEGF13, which results in a variant of Marfan syndrome, a connective tissue disease. Previous experiments on isolated cbEGF13 and a cbEGF13-14 pair indicated that the G1127S mutation caused defective folding of cbEGF13 but not cbEGF14. We have used limited proteolysis methods and two-dimensional NMR spectroscopy to identify the structural consequences of this mutation in a covalently linked cbEGF12-13 pair and a cbEGF12-14 triple domain construct. Protease digestion studies of the cbEGF12-13 G1127S mutant pair indicated that both cbEGF12 and 13 retained similar calcium binding properties and thus tertiary structure to the normal domain pair, because all identified cleavage sites showed calcium-dependent protection from proteolysis. However, small changes in the conformation of cbEGF13 G1127S, revealed by the presence of a new protease-sensitive site and comparative two-dimensional NOESY data, suggested that the fold of the mutant domain was not identical to the wild-type, but was native-like. Additional cleavage sites identified in cbEGF12-14 G1127S indicated further subtle changes within the mutant domain but not the flanking domains. We have concluded the following in this study. (i) Covalent linkage of cbEGF12 preserves the native-like fold of cbEGF13 G1127S and (ii) conformational effects introduced by G1127S are localized to cbEGF13. This study demonstrates that missense mutations in fibrillin-1 cbEGF domains can cause short range structural effects in addition to long range effects previously observed with a E1073K mutation in cbEGF12.
Analysis and visualization of single‐trial event‐related potentials

In this study, a linear decomposition technique, independent component analysis (ICA), is applied to single‐trial multichannel EEG data from event‐related potential (ERP) experiments. Spatial filters derived by ICA blindly separate the input data into a sum of temporally independent and spatially fixed components arising from distinct or overlapping brain or extra‐brain sources. Both the data and their decomposition are displayed using a new visualization tool, the “ERP image,” that can clearly characterize single‐trial variations in the amplitudes and latencies of evoked responses, particularly when sorted by a relevant behavioral or physiological variable. These tools were used to analyze data from a visual selective attention experiment on 28 control subjects plus 22 neurological patients whose EEG records were heavily contaminated with blink and other eye‐movement artifacts. Results show that ICA can separate artifactual, stimulus‐locked, response‐locked, and non‐event‐related background EEG activities into separate components, a taxonomy not obtained from conventional signal averaging approaches. This method allows: (1) removal of pervasive artifacts of all types from single‐trial EEG records, (2) identification and segregation of stimulus‐ and response‐locked EEG components, (3) examination of differences in single‐trial responses, and (4) separation of temporally distinct but spatially overlapping EEG oscillatory activities with distinct relationships to task events. The proposed methods also allow the interaction between ERPs and the ongoing EEG to be investigated directly. We studied the between‐subject component stability of ICA decomposition of single‐trial EEG epochs by clustering components with similar scalp maps and activation power spectra. Components accounting for blinks, eye movements, temporal muscle activity, event‐related potentials, and event‐modulated alpha activities were largely replicated across subjects. Applying ICA and ERP image visualization to the analysis of sets of single trials from event‐related EEG (or MEG) experiments can increase the information available from ERP (or ERF) data. Hum. Brain Mapping 14:166–185, 2001. © 2001 Wiley‐Liss, Inc.
Relationship between psychological distress and resilience in rescue workers

Objectives: To assess the relationship between psychological distress and resilience in rescue workers. Following hypothesis was formulated; there would be negative correlation between psychological distress and resilience in rescue workers. Method: A correlational study was conducted from June-August 2015 in Rahim Yar Khan, Punjab, Pakistan. The sample of the present study consisted of 100 rescue workers. The age of the participants ranged from 23 to 40 year old with the mean age of 27.4±3.9 years. Demographic information form, Kessler psychological distress scale and adult resilience measure were administered on the participants to assess the level of psychological distress and resilience. Results: Pearson product moment coefficient of correlation was applied to analyze the relationship of psychological distress and resilience. Analysis of the result indicated that there is negative relationship between psychological distress and resilience (r= -0.203, p<0.01) in rescue workers. Further, contextual factors (r= -0.292, p<0.05) and its subcomponents including spiritual beliefs (r= -0.239, p<0.05) and cultural resources (r= -0.287, p<0.01) were also found to be inversely correlated with psychological distress. Conclusion: The research evidenced that rescue workers were experiencing psychological distress Resilience factors should be considered while designing trainings to preserve mental health and to enhance the psychological well-being of rescue workers.
Differential sensitivity of cones to iron-mediated oxidative damage.

PURPOSE In this study, the hypothesis that increased intraocular levels of iron cause oxidative damage to the retina was tested. METHODS Adult C57BL/6 mice were given an intravitreous injection of saline or 0.10, 0.25, or 0.50 mM FeSO(4). Scotopic electroretinograms (ERGs) were performed 3, 7, and 14 days after injection, and photopic ERGs were performed on day 14. Hydroethidine was used to identify superoxide radicals and lipid peroxidation was visualized by staining for hydroxynonenal (HNE). Retinal cell death was evaluated by TUNEL and measurement of inner nuclear layer (INL) and outer nuclear layer (ONL) thickness. Levels of rhodopsin and cone-opsin mRNA were measured by quantitative real time RT-PCR. Cone density was assessed by peanut agglutinin staining and confocal microscopy. RESULTS Compared with retinas in saline-injected eyes, retinas from eyes injected with FeSO(4) showed greater fluorescence after intravenous injection of hydroethidine due to superoxide radicals in photoreceptors, greater photoreceptor staining for HNE, a marker of lipid peroxidation, and increased expression of Heme oxygenase 1, an indicator of oxidative stress. ERG b-wave amplitudes were reduced (photopic > scotopic) in FeSO(4)-injected eyes compared with those in saline-injected eyes. Numerous TUNEL-stained nuclei were seen along the outer border of the ONL, the location of cone cell nuclei, at 1 and 2 days after injection of FeSO(4). In FeSO(4)-injected eyes, the thickness of the ONL, but not the INL, was significantly reduced, and 17 days after injection, there were 3.8- and 2.6-fold reductions in the mRNAs for M-cone and S-cone opsin, respectively, whereas there was no significant difference in rhodopsin mRNA. Confocal microscopy of peanut agglutinin-stained sections showed dose-dependent FeSO(4)-induced cone drop out. CONCLUSIONS Increased intraocular levels of FeSO(4) cause oxidative damage to photoreceptors with greater damage to cones than rods. This finding suggests that the oxidative defense system of cones differs from that of rods and other retinal cells, and that cones are more susceptible to damage from the type of oxidative stress imposed by iron.
Sdf1/Cxcr4 signaling controls the dorsal migration of endodermal cells during zebrafish gastrulation

During vertebrate gastrulation, both mesodermal and endodermal cells internalize through the blastopore beneath the ectoderm. In zebrafish, the internalized mesodermal cells move towards the dorsal side of the gastrula and, at the same time, they extend anteriorly by convergence and extension (C&E) movements. Endodermal cells showing characteristic filopodia then migrate into the inner layer within the hypoblast next to the yolk syncytial layer (YSL). However, little is known about how the movement of endodermal cells is regulated during gastrulation. Here we show that sdf1a- and sdf1b-expressing mesodermal cells control the movements of the cxcr4a-expressing endodermal cells. The directional migration of endodermal cells during gastrulation is inhibited by knockdown of either cxcr4a or sdf1a/sdf1b (sdf1). We also show that misexpressed Sdf1 acts as a chemoattractant for cxcr4a-expressing endodermal cells. We further found, using the endoderm-specific transgenic line Tg(sox17:EGFP), that Sdf1/Cxcr4 signaling regulates both the formation and orientation of filopodial processes in endodermal cells. Moreover, the accumulation of phosphoinositide 3,4,5-trisphosphate (PIP3), which is known to occur at the leading edge of migrating cells, is not observed at the filopodia of endodermal cells. Based on our results, we propose that sdf1-expressing mesodermal cells, which overlie the endodermal layer, guide the cxcr4a-expressing endodermal cells to the dorsal side of the embryo during gastrulation, possibly through a PIP3-independent pathway.
Cardiovascular and Cerebrovascular Aging – New Mechanisms and Insights The TRPA 1 channel is a cardiac target of mIGF-1 / SIRT 1 signaling

Valerio Pazienza,* Cristoforo Pomara,* Francesco Cappello, Raffaele Calogero, Matteo Carrara, Gianluigi Mazzoccoli,* and Manlio Vinciguerra* Division of Gastroenterology, Department of Medical Sciences, IRCCS Scientific Institute “Casa Sollievo della Sofferenza,” San Giovanni Rotondo, Italy; Department of Anatomy, University of Malta, Msida, Malta; Department of Forensic Pathology, University of Foggia, Foggia, Italy; Department of Experimental Medicine and Clinical Neuroscience, Section of Human Anatomy, University of Palermo, Palermo, Italy; Euro-Mediterranean Institute of Science and Technology, Palermo, Italy; Molecular Biotechnology Center, University of Turin, Turin, Italy; Division of Internal Medicine and Chronobiology Unit, Department of Medical Sciences, IRCCS Scientific Institute “Casa Sollievo della Sofferenza,” San Giovanni Rotondo, Italy; and Division of Medicine, University College London, London, United Kingdom.
INS/Wi-Fi based indoor navigation using adaptive Kalman filtering and vehicle constraints

Due to the complementary nature of inertial navigation system (INS) and Wi-Fi positioning principles, an INS/Wi-Fi integrated system is expected to form a low-cost and continuous indoor navigation solution with better performance than using the standalone systems. In this paper, we explore the integration of Wi-Fi measurements with data from microelectromechanical systems (MEMS) based inertial measurement unit (IMU) for indoor vehicle navigation. Two enhancements, which employ adaptive Kalman filtering (AKF) and vehicle constraints, for supporting the integrated system are presented. One field experiment has been conducted for estimating the trajectory of a mobile robot vehicle. The numerical results show that the enhanced integrated system provides higher navigation accuracy, compared to using standalone Wi-Fi positioning and conventional INS/Wi-Fi integration.
The adaptive bases algorithm for intensity-based nonrigid image registration

Nonrigid registration of medical images is important for a number of applications such as the creation of population averages, atlas-based segmentation, or geometric correction of functional magnetic resonance imaging (IMRI) images to name a few. In recent years, a number of methods have been proposed to solve this problem, one class of which involves maximizing a mutual information (Ml)-based objective function over a regular grid of splines. This approach has produced good results but its computational complexity is proportional to the compliance of the transformation required to register the smallest structures in the image. Here, we propose a method that permits the spatial adaptation of the transformation's compliance. This spatial adaptation allows us to reduce the number of degrees of freedom in the overall transformation, thus speeding up the process and improving its convergence properties. To develop this method, we introduce several novelties: 1) we rely on radially symmetric basis functions rather than B-splines traditionally used to model the deformation field; 2) we propose a metric to identify regions that are poorly registered and over which the transformation needs to be improved; 3) we partition the global registration problem into several smaller ones; and 4) we introduce a new constraint scheme that allows us to produce transformations that are topologically correct. We compare the approach we propose to more traditional ones and show that our new algorithm compares favorably to those in current use.
Impact of aftertreatment devices on primary emissions and secondary organic aerosol formation potential from in-use diesel vehicles: results from smog chamber experiments

Abstract. Diesel particulate matter (DPM) is a significant source of aerosol in urban areas and has been linked to adverse health effects. Although newer European directives have introduced increasingly stringent standards for primary PM emissions, gaseous organics emitted from diesel cars can still lead to large amounts of secondary organic aerosol (SOA) in the atmosphere. Here we present results from smog chamber investigations characterizing the primary organic aerosol (POA) and the corresponding SOA formation at atmospherically relevant concentrations for three in-use diesel vehicles with different exhaust aftertreatment systems. One vehicle lacked exhaust aftertreatment devices, one vehicle was equipped with a diesel oxidation catalyst (DOC) and the third vehicle used both a DOC and diesel particulate filter (DPF). The experiments presented here were obtained from the vehicles at conditions representative of idle mode, and for one car in addition at a speed of 60 km/h. An Aerodyne high-resolution time-of-flight aerosol mass spectrometer (HR-ToF-AMS) was used to measure the organic aerosol (OA) concentration and to obtain information on the chemical composition. For the conditions explored in this paper, primary aerosols from vehicles without a particulate filter consisted mainly of black carbon (BC) with a low fraction of organic matter (OM, OM/BC
Yotiao, a Novel Protein of Neuromuscular Junction and Brain That Interacts with Specific Splice Variants of NMDA Receptor Subunit NR1

The molecular machinery underlying neurotransmitter receptor immobilization at postsynaptic sites is poorly understood. The NMDA receptor subunit NR1 can form clusters in heterologous cells via a mechanism dependent on the alternatively spliced C1 exon cassette in its intracellular C-terminal tail, suggesting a functional interaction between NR1 and the cytoskeleton. The yeast two-hybrid screen was used here to identify yotiao, a novel coiled coil protein that interacts with NR1 in a C1 exon-dependent manner. Yotiao mRNA (11 kb) is present modestly in brain and abundantly in skeletal muscle and pancreas. On Western blots, yotiao appears as an ∼230 kDa band that is present in cerebral cortex, hippocampus, and cerebellum. Biochemical studies reveal that yotiao fractionates with cytoskeleton-associated proteins and with the postsynaptic density. With regard to immunohistochemistry, two anti-yotiao antibodies display a somatodendritic staining pattern similar to each other and to the staining pattern of NR1. Yotiao was colocalized by double-label immunocytochemistry with NR1 in rat brain and could be coimmunoprecipitated with NR1 from heterologous cells. Thus yotiao is an NR1-binding protein potentially involved in cytoskeletal attachment of NMDA receptors. Consistent with a general involvement in postsynaptic structure, yotiao was also found to be specifically concentrated at the neuromuscular junction in skeletal muscle.
Selective Degeneration of Purkinje Cells with Lewy Body-Like Inclusions in Aged NFHLACZ Transgenic Mice

Transgenic (NFHLacZ) mice expressing a fusion protein composed of a truncated high-molecular-weight mouse neurofilament (NF) protein (NFH) fused to β-galactosidase (LacZ) develop inclusions in neurons throughout the CNS. These inclusions persist from birth to advanced age and contain massive filamentous aggregates including all three endogenous NF proteins and the NFHLacZ fusion protein. Further, the levels of endogenous NF proteins are selectively reduced in NFHLacZ mice. Because these inclusions resemble NF-rich Lewy bodies (LBs) in Parkinson’s disease and LB dementia, we asked whether these lesions compromised the viability of affected neurons during aging. We studied hippocampal CA1 neurons, nearly all of which harbored inclusions (type I) devoid of cellular organelles, and cerebellar Purkinje cells, nearly all of which accumulated inclusions (type II) containing numerous entrapped organelles. Purkinje cells with type II inclusions began to degenerate in the NFHLacZ mice at ∼1 year of age, and most were eliminated by 18 months of age. In contrast, there was no significant loss of type I inclusion-bearing CA1 neurons with age. These data suggest that the sequestration of cellular organelles in type II inclusions may isolate and impair the function of these organelles, thereby rendering Purkinje cells selectively vulnerable to degeneration with age as in neurodegenerative diseases of the elderly characterized by accumulation of LBs.
Proxy ecology - cooperative proxies with artificial life

In this paper, we propose a novel P2P cooperative proxy cache system using an individual-based model. We borrow the idea from an ecological system as well as economic systems to manage the cooperative proxies through data and information exchange among individual proxies. The data flow among proxy nodes creates artificial life for the cooperative proxies. The proxy servers with artificial life can automatically configure themselves into a virtual proxy graph. The aggregate effect of caching actions by individual peer proxies automatically distributes the Web document closer to the clients and balances the workload. Our simulation results show that the proposed proxy caching scheme tremendously improves the system performance. In addition, the individual-based design model ensures the simplicity and scalability of the cache system.
Magnetotelluric soundings along the COCORP seismic profile in the central Rio Grande rift

Every fall since 1950, the New Mexico Geological Society (NMGS) has held an annual Fall Field Conference that explores some region of New Mexico (or surrounding states). Always well attended, these conferences provide a guidebook to participants. Besides detailed road logs, the guidebooks contain many well written, edited, and peer-reviewed geoscience papers. These books have set the national standard for geologic guidebooks and are an essential geologic reference for anyone working in or around New Mexico.
Interdependent Minds: The Dynamics of Close Relationships

H. T. Reis, Foreword. 1. Motivating Responsiveness: Why a Smart Relationship Unconscious? 2. Procedural Rules for Responsiveness: The Motivation-Management Model. 3. Trust: When to Approach? 4. Commitment: How Close a Connection? 5. The Situational Risks: Seek Connection or Avoid Rejection? 6. The Rules for Seeking Connection: Increase and Justify Own Dependence. 7. The Rules for Avoiding Rejection: Withhold Own and Promote Partner Dependence. 8. Relationship Personality: Making Certain Rules a Habit. 9. Being Swept Away: How Passionate Love Makes It Natural to Connect. 10. Being Mowed Over: How Real Life Makes It Natural to Self-protect. 11. How the Person, the Pairing, and the Context Make (or Break) Relationships. 12. A Practical Guide for Relationships.
Introduction to Personality

In this course, I want to provide a critical analysis of the most significant, enduring and controversial issues in the areas of personality and clinical psychology. Topics include: the meaning of normality, abnormality, and deviance; the units for conceptualizing persons; alternative models of human nature; the nature and role of dispositions; the structure of consistency in personality; the development and maintenance of personality problems; defense and the coping process; self-regulatory processes, willpower, and ego development; continuity and change in development; the nature of the self; clinical inference and evidence; prediction of behavior; the nature of the unconscious and self-knowledge; the rationale underlying alternative treatment strategies; the assessment and therapeutic modification of selected personality problems; the relations between personality psychology as a science and clinical psychology as a profession.