Miracle-dz/UniFAR-FTUs huggingface dataset:
Hemopexin and haptoglobin: allies against heme toxicity from hemoglobin not contenders

The goal here is to describe our current understanding of heme metabolism and the deleterious effects of “free” heme on immunological processes, endothelial function, systemic inflammation, and various end-organ tissues (e.g., kidney, lung, liver, etc.), with particular attention paid to the role of hemopexin (HPX). Because heme toxicity is the impetus for much of the pathology in sepsis, sickle cell disease (SCD), and other hemolytic conditions, the biological importance and clinical relevance of HPX, the predominant heme binding protein, is reinforced. A perspective on the function of HPX and haptoglobin (Hp) is presented, updating how these two proteins and their respective receptors act simultaneously to protect the body in clinical conditions that entail hemolysis and/or systemic intravascular (IVH) inflammation. Evidence from longitudinal studies in patients supports that HPX plays a Hp-independent role in genetic and non-genetic hemolytic diseases without the need for global Hp depletion. Evidence also supports that HPX has an important role in the prognosis of complex illnesses characterized predominantly by the presence of hemolysis, such as SCD, sepsis, hemolytic-uremic syndrome, and conditions involving IVH and extravascular hemolysis (EVH), such as that generated by extracorporeal circulation during cardiopulmonary bypass (CPB) and from blood transfusions. We propose that quantitating the amounts of plasma heme, HPX, Hb-Hp, heme-HPX, and heme-albumin levels in various disease states may aid in the diagnosis and treatment of the above-mentioned conditions, which is crucial to developing targeted plasma protein supplementation (i.e., “replenishment”) therapies for patients with heme toxicity due to HPX depletion.
CONGENITAL HYPOPLASIA OF THE UPPER FEMUR.

1. The surgical management of two children with congenital hypoplasia of the upper end of the femur is described.2. Early exploration is advocated to establish the nature and extent of the anomaly and to attempt its correction.3. The preliminary results are sufficiently encouraging for us to recommend that further attempts at surgical treatment be considered in patients with this disorder.
Genomic consequences of genetic rescue in an insular population of bighorn sheep (Ovis canadensis)

Genetic rescue is a management intervention whereby a small population is supplemented with individuals from other populations in an attempt to reverse the effects of inbreeding and increased genetic load. One such rescue was recently documented in the population of bighorn sheep (Ovis canadensis) within the National Bison Range wildlife refuge (Montana, USA). Here, we examine the locus‐specific effects of rescue in this population using a newly developed genome‐wide set of 195 microsatellite loci and first‐generation linkage map. We found that the rate of introgression varied among loci and that 111 loci, 57% of those examined, deviated from patterns of neutral inheritance. The most common deviation was an excess of homozygous genotypes relative to neutral expectations, indicative of directional selection. As in previous study of this rescue, individuals with more introduced alleles had higher reproductive success and longevity. In addition, we found 30 loci, distributed throughout the genome, which seem to have individual effects on these life history traits. Although the potential for outbreeding depression is a major concern when translocating individuals between populations, we found no evidence of such effects in this population.
A new method for modeling and solving the protein fold recognition problem (extended abstract)

Computational recognition of native-like folds from a protein fold database is considered to be a promising alternative approach to the ab initio fold prediction. We present a new and egective method forprotein fold recognition through optimally aligning (threading) an amino acid sequence and a protein fold (template). A protein fold, in our database, is represented as a se953 of core secondary structures, and the alignment quality is cletermined by three factors. They are (I) the fitness between each amino acid and the environment of its assigned (aligned) template position; (2) pairwise interaction preferences between amino acids that are spatially close,and (3) alignment gap penalties. Our threading algorithm cons&ucts an optimum alignment between an amino acid sequence of size n and a protein fold template of size m in O((m-l-n1+o-5cMlog(n))nc+1) time and O(nm+nc+2) space, where M is the number of core secondary structures in the fold, and C is a (small) nonnegative integer, determined by a mathematical property of the pairwise interactions in the fold. C is less than or equal to 4 for about 75% of the 296 unique folds in our . database, when pairwise interactions are restricted to amino acids 5 7A apart (measured between their beta carbon atoms). An approximation scheme is developed for fold templates with C > 4, when threading requires too much memo y and time to be practical on a typical workstation.
Dynamics and control of a class of underactuated mechanical systems

This paper presents a theoretical framework for the dynamics and control of underactuated mechanical systems, defined as systems with fewer inputs than degrees of freedom. Control system formulation of underactuated mechanical systems is addressed and a class of underactuated systems characterized by nonintegrable dynamics relations is identified. Controllability and stabilizability results are derived for this class of underactuated systems. Examples are included to illustrate the results; these examples are of underactuated mechanical systems that are not linearly controllable or smoothly stabilizable.
n in vitro test of the efficacy of silver-containing wound dressings gainst Staphylococcus aureus and Pseudomonas aeruginosa in imulated wound fluid

An isothermal microcalorimetric assay was used to quantify the efficacy of a silver-containing wound dressing against two common wound pathogens, Pseudomonas aeruginosa and Staphylococcus aureus. The growth patterns of the two species were unique and varied depending on the environment in which the organisms were grown. Addition of non-silver-containing dressing altered the growth kinetics while addition of silver (contained either in a dressing or as AgNO3 solution) was seen to elicit inhibition and/or kill depending on concentration. Tests were conducted in nutrient broth and simulated wound fluid. It
Energy-Efficient, Utility Accrual Real-Time Scheduling

In this dissertation, we consider timeliness and energy optimization in battery-powered, mobile embedded real-time systems. We focus on real-time systems that operate in environments with dynamically uncertain properties, including context-dependent activity execution times and arbitrary activity arrival patterns. We consider an application model where activities are subject to time/utility function (or TUF) time constraints, mutual exclusion constraints on concurrent sharing of non-CPU resources, timeliness requirements including assurances on individual activity timeliness behavior, and system-level energy consumption requirements including a non-exhaustable energy budget. To account for uncertainties in activity properties in dynamic systems, we stochastically describe activity execution demands, and describe activity arrival behaviors using the uni-modal arbitrary arrival model, which allows unbounded arrival frequencies. We consider the scheduling optimality criteria of: (1) probabilistically satisfying lower bounds on individual activities' maximal timeliness utilities, and (2) maximizing system-level energy efficiency, while ensuring that the system's energy consumption never exhausts the energy budget and resource mutual exclusion constraints are satisfied. For this multi-criteria scheduling problem, we present a DVS (dynamic voltage scaling)-based, real-time scheduling algorithm called the Energy-Bounded Utility Accrual Algorithm (or EBUA). Since the scheduling problem is NP -hard, EBUA heuristically (and dynamically) allocates CPU cycles to activities, computes activity schedules, and scales CPU voltage and frequency with a polynomial-time cost. If activities' cumulative execution demands exceed the available CPU time or may exhaust the system's energy budget, the algorithm defers and rejects jobs in a controlled fashion, minimizing system-level energy consumption and maximizing total accrued utility. We analytically establish several properties of EBUA. We prove that the algorithm never exhausts the specified energy budget. Further, we establish EBUA's timeliness optimality during under-loads, freedom from deadlocks, and correctness in mutually exclusive resource sharing. In particular, we prove that the algorithm's timeliness behavior subsumes the optimal timeliness behavior of deadline scheduling as a special case, and identify the conditions under which lower bounds on individual activity utilities are satisfied. In addition, we upper bound the time needed for mutually exclusively accessing shared resources under EBUA. We conduct experimental studies by simulating the algorithm on the DVS-enabled AMD k6 processor model, and by implementing it on QNX Neutrino 6.2. 1 RTOS. Our experimental results validate our analytical results. Further, they confirm EBUA's superiority over other energy-efficient real-time scheduling algorithms on timeliness and energy consumption behaviors.
3. Law, Lawyers, and Legal Practice in Silicon Valley: A Preliminary Report

What do lawyers contribute to technological change and economic development? Much popular opinion assumes that the contribution is mostly negative, that the vast amounts of legal time billed to corporate enterprise ($38 billion worth annually, according to a recent estimate)' are the pathological symptoms of an over-regulated, excessively litigious culture that diverts resources from productivity and innovation into wasteful paperpushing.2 Other, more sanguine observers-usually lawyers-argue to the contrary that legal services are valuable, even indispensable parts of the infrastructure that support the efficiency of transactions, even if their value is not always appreciated by clients or the general public. 3 The debate has been chiefly at the level of assertion, because there has been so little serious research since James Willard Hurst's monumental study in 1964 of the ways in which lawmakers and lawyers designed and operated the legal-institutional frameworks for the growth and organization of the lumber industry in nineteenth century Wisconsin.4 Studies of the "legal profession" tend to focus on the organization, entry policies, education and ethics of the bar. Although some excellent work has recently appeared on the social structure of the bar and the internal organization and cultures of law firms,5 there is still almost no scholarly research into lawyers' actual work tasks. So before approaching the grand questions of how lawyers facilitate or parasitically feed off economic growth, we need to have reliable pictures of their practices, of the ordinary jobs they do for their business clients,
Structural Peculiarities of Human Genes Which Expression Increases in Response to Stress

We studied structural peculiarities of 123 human genes which were previously identified as genes of early response to exercise stress. Compared to protein-coding genes in general, their structure revealed some peculiarities: they are shorter in both coding and non-coding regions and contain fewer introns. This result is in good agreement with the similar results reported for stress-responding genes in other species (yeasts, thale cress, and mice).
Software reuse and plagiarism: a code of practice

In general, university guidelines or policies on plagiarism are not sufficiently detailed to cope with the technical complexity of software. Software plagiarism can have a significant impact on a student's degree result, particularly in courses were there is a significant emphasis on large-scale projects. We argue that a policy for software reuse is the most explicit, and fair, way of overcoming this problem. In our policy, we specify the notion of software to cover all the documents that are generally built during the engineering of a software system -- analysis, requirements, validation, design, verification, implementation and tests. Examples are used to show acceptable and unacceptable forms of reuse, mostly at the design, testing and implementation stages. These examples are represented in Java, although they should be easily understood by anyone with software engineering experience. We conclude with a simple code of practice for reuse of software based on a file-level policy, combined with emphasis on re-using only what is rigorously verified.
A framework to address a two-dimensional composition of concerns 1

Although not bound to Object-Oriented Programming (OOP), Aspect-Oriented Programming (AOP) is a paradigm proposal that retains the advantages of OOP and aims at avoiding the tyranny of dominant decomposition. The goal is to achieve an improved separation of concerns in both design, and implementation. Our work concentrates on the aspectual decomposition of concurrent object-oriented systems. We address composition of concerns by the aspect moderator class that coordinates the interaction of components and aspects while preserving the semantics of the overall system. Our design framework provides an adaptable model that allows for an open language where new aspects (specifications) can be added and their semantics can be delivered to the compiler through the moderator. In essence the aspect moderator framework is a program that extends the language itself.
Birds are tracking climate warming, but not fast enough

Range shifts of many species are now documented as a response to global warming. But whether these observed changes are occurring fast enough remains uncertain and hardly quantifiable. Here, we developed a simple framework to measure change in community composition in response to climate warming. This framework is based on a community temperature index (CTI) that directly reflects, for a given species assemblage, the balance between low- and high-temperature dwelling species. Using data from the French breeding bird survey, we first found a strong increase in CTI over the last two decades revealing that birds are rapidly tracking climate warming. This increase corresponds to a 91 km northward shift in bird community composition, which is much higher than previous estimates based on changes in species range edges. During the same period, temperature increase corresponds to a 273 km northward shift in temperature. Change in community composition was thus insufficient to keep up with temperature increase: birds are lagging approximately 182 km behind climate warming. Our method is applicable to any taxa with large-scale survey data, using either abundance or occurrence data. This approach can be further used to test whether different delays are found across groups or in different land-use contexts.
The Internet: A Philosophical Inquiry

The Internet: A Philosophical Inquiry develops many of the themes Gordon Graham presented in his highly successful radio series, The Silicon Society. Exploring the tensions between the warnings of the Neo-Luddites and the bright optimism of the Technophiles, Graham offers the first concise and accessible exploration of the issues which arise as we enter further into the world of Cyberspace. This original and fascinating study takes us to the heart of questions that none of us can afford to ignore: how does the Internet affect our concepts of identity, moral anarchy, censorship, community, democracy, virtual reality and imagination? Free of jargon and full of stimulating ideas, this is essential reading for anyone wishing to think clearly and informatively about the complexities of our technological future.
Accurate computation of the smallest eigenvalue of a diagonally dominant M-matrix

If each off-diagonal entry and the sum of each row of a diagonally dominant M-matrix are known to certain relative accuracy, then its smallest eigenvalue and the entries of its inverse are known to the same order relative accuracy independent of any condition numbers. In this paper, we devise algorithms that compute these quantities with relative errors in the magnitude of the machine precision. Rounding error analysis and numerical examples are presented to demonstrate the numerical behaviour of the algorithms.
A new choleretic effect of folinic acid.

BACKGROUND/AIMS In the chemotherapy of recurrent gastric cancer with 5-fluorouracil and folinic acid, an interesting phenomenon, the reduction of jaundice and improvement of liver function, was observed. The aim of this study was to investigate the mechanism of this phenomenon, and to confirm a choleretic effect of folinic acid. METHODOLOGY The bile duct of anesthetized rats was catheterized, and bile was collected. Bile volume and total bile acid production following intraperitoneal administration of folinic acid were determined and compared to those of control rats. RESULTS Both bile volume and total bile acid production increased following intraabdominal administration of folinic acid. CONCLUSIONS Folinic acid has a newly described pharmacologic effect of stimulating bile acid-dependent choleresis. It is possible that folinic acid may become a new drug for the treatment of jaundice or for the improvement of overall liver function.
Preliminary draft Short-Term Debt and Bank Risk

The extant literature has suggested that one of the main causes of the recent financial crisis has been the excessive use of short-term debt by financial institutions. Using a large sample of U.S. commercial banks we find that increases in repurchase agreements (repos) was recognized by external capital markets to increase bank risk in the pre-crisis period. No such effect is found for other forms of short-term debt such as commercial paper, brokered deposits and demand deposits. The importance of repos to increasing bank risk is consistent with the argument of Gorton and Metrick (2012a, b) who found a significant “run” in the repo market. In the crisis, we find a negative relationship between repos and bank risk. This is because good banks were able to continue funding their repos, whereas bad banks had to significantly decrease their repo funding. Counter to the notion that liquid assets provided a buffer against shocks, we find that banks’ were unable to reduce their risk either in the pre-crisis or crisis period.
Partial transformation from fast to slow muscle fibers induced by deafferentation of capsaicin‐sensitive muscle afferents

Mechanical and histochemical characteristics of the lateral gastrocnemius (LG) muscle of the rat were examined 21 days after capsaicin injection into the LG muscle. The capsaicin caused a decrease in generation rate of twitch and tetanic tension and an increase in fatigue resistance of LG muscle. The histochemical muscle fiber profile evaluated by myosin adenosine triphosphatase and reduced nicotinamide adenine dinucleotide tetrazolium reductase methods showed an increase of type I and IIC fibers and a decrease of the type IIB in whole muscle, and a decrease of the IIA, IIX fibers in the red part accompanied by their increase in the white part. Therefore the capsaicin treatment, which selectively eliminated fibers belonging to the III and IV groups of muscle afferents, induced muscle fiber transformation from fast contracting fatiguing fibers to slowly contracting nonfatiguing ones. © 1997 John Wiley & Sons, Inc. Muscle Nerve 20: 1404–1413, 1997
A Scale for the Assessment of Hedonic Tone the Snaith–Hamilton Pleasure Scale

Background Hedonic tone and its absence, anhedonia, are important in psychopathological research, but instruments for their assessment are lengthy and probably culturally biased. Method A new scale was constructed from the responses of a large sample of the general population to a request to list six situations which afforded pleasure. The most frequent items were reviewed and those likely to be affected by cultural setting, age, or sex were removed. A pilot study led to an abbreviated scale of 14 items, covering four domains of pleasure response. This questionnaire was subjected to psychometric evaluation in new samples from the general population and psychiatric patients. Results The scale was found to have a score range that would distinguish a ‘normal’ from an ‘abnormal’ response. Validity and reliability were found to be satisfactory. Conclusions The new scale, the Snaith-Hamilton Pleasure Scale (SHAPS), is an instrument which may be recommended for psychopathological research.
Layer 4 Pyramidal Neurons Exhibit Robust Dendritic Spine Plasticity In Vivo after Input Deprivation

Pyramidal neurons in layers 2/3 and 5 of primary somatosensory cortex (S1) exhibit somewhat modest synaptic plasticity after whisker input deprivation. Whether neurons involved at earlier steps of sensory processing show more or less plasticity has not yet been examined. Here, we used longitudinal in vivo two-photon microscopy to investigate dendritic spine dynamics in apical tufts of GFP-expressing layer 4 (L4) pyramidal neurons of the vibrissal (barrel) S1 after unilateral whisker trimming. First, we characterize the molecular, anatomical, and electrophysiological properties of identified L4 neurons in Ebf2-Cre transgenic mice. Next, we show that input deprivation results in a substantial (∼50%) increase in the rate of dendritic spine loss, acutely (4–8 d) after whisker trimming. This robust synaptic plasticity in L4 suggests that primary thalamic recipient pyramidal neurons in S1 may be particularly sensitive to changes in sensory experience. Ebf2-Cre mice thus provide a useful tool for future assessment of initial steps of sensory processing in S1.
Using real‐time MRI to quantify altered joint kinematics in subjects with patellofemoral pain and to evaluate the effects of a patellar brace or sleeve on joint motion

Abnormal patellofemoral joint motion is a possible cause of patellofemoral pain, and patellar braces are thought to alleviate pain by restoring normal joint kinematics. We evaluated whether females with patellofemoral pain exhibit abnormal patellofemoral joint kinematics during dynamic, weight‐bearing knee extension and assessed the effects of knee braces on patellofemoral motion. Real‐time magnetic resonance (MR) images of the patellofemoral joints of 36 female volunteers (13 pain‐free controls, 23 patellofemoral pain) were acquired during weight‐bearing knee extension. Pain subjects were also imaged while wearing a patellar‐stabilizing brace and a patellar sleeve. We measured axial‐plane kinematics from the images. Females with patellofemoral pain exhibited increased lateral translation of the patella for knee flexion angles between 0°and 50° (p = 0.03), and increased lateral tilt for knee flexion angles between 0° and 20° (p = 0.04). The brace and sleeve reduced the lateral translation of the patella; however, the brace reduced lateral displacement more than the sleeve (p = 0.006). The brace reduced patellar tilt near full extension (p = 0.001), while the sleeve had no effect on patellar tilt. Our results indicate that some subjects with patellofemoral pain exhibit abnormal weight‐bearing joint kinematics and that braces may be effective in reducing patellar maltracking in these subjects. Published by Wiley Periodicals, Inc. J Orthop Res 27: 571–577, 2009