Miracle-dz/UniFAR-FTUs huggingface dataset:
A 3‐D Semianalytical Solution for Density‐Driven Flow in Porous Media

Existing analytical and semianalytical solutions for density‐driven flow (DDF) in porous media are limited to 2‐D domains. In this work, we develop a semianalytical solution using the Fourier Galerkin method to describe DDF induced by salinity gradients in a 3‐D porous enclosure. The solution is constructed by deriving the vector potential form of the governing equations and changing variables to obtain periodic boundary conditions. Solving the 3‐D spectral system of equations can be computationally challenging. To alleviate computations, we develop an efficient approach, based on reducing the number of primary unknowns and simplifying the nonlinear terms, which allows us to simplify and solve the problem using only salt concentration as primary unknown. Test cases dealing with different Rayleigh numbers are solved to analyze the solution and gain physical insight into 3‐D DDF processes. In fact, the solution displays a 3‐D convective cell (actually a vortex) that resembles the quarter of a torus, which would not be possible in 2‐D. Results also show that 3‐D effects become more important at high Rayleigh number. We compare the semianalytical solution to research (Transport of RadioACtive Elements in Subsurface) and industrial (COMSOL Multiphysics®) codes. We show cases (high Raleigh number) where the numerical solution suffers from numerical artifacts, which highlight the worthiness of our semianalytical solution for code verification and benchmarking. In this context, we propose quantitative indicators based on several metrics characterizing the fluid flow and mass transfer processes and we provide open access to the source code of the semianalytical solution and to the corresponding numerical models.
Urinary incontinence.

In both primary and secondary care, other conditions have to be excluded before the diagnosis can be made: • Recurrent urinary tract infections (UTIs) • Bladder outflow obstruction. This is uncommon in women unless there is there is a history of pelvic or incontinence surgery • Severe chronic constipation can cause a physical outflow obstruction • Psychological and metabolic causes of polydipsia and polyuria such as diabetes mellitus, diabetes insipidus or excessive fluid consumption • Neurological abnormalities (spinal cord injuries, spina bifida, multiple sclerosis or upper motor neurone disease) • Drugs, medications (eg. diuretics, ACE inhibitors, etc).
Endocytosis, membrane recycling and sorting of GPI‐anchored proteins: Trypanosoma brucei as a model system

In the flagellated protozoon Trypanosoma brucei, endo‐ and exocytosis are restricted to a small area of the plasma membrane, the flagellar pocket. All endosomal compartments and the single Golgi complex are located within the posterior part of the cell between the flagellar pocket and the nucleus. The use of reverse genetic tools, including RNA interference, in combination with quantitative 3D‐fluorescence and electron microscopic techniques has provided an insight into endosomal membrane traffic, which occurs at a very high rate and appears to exhibit a lower level of complexity than in mammalian cells. The flagellate is an excellent model system for studies on endocytosis, sorting and recycling of glycosylphosphatidylinositol‐anchored glycoproteins, because 107 molecules of the variant surface glycoprotein form a dense coat at the cell's surface. Because the endocytic rate varies widely at different stages in the parasite's life cycle, trypanosomes may be used for investigating developmental aspects of their endocytic system.
Dynamics of Mechanical Signal Transmission through Prestressed Stress Fibers

Transmission of mechanical stimuli through the actin cytoskeleton has been proposed as a mechanism for rapid long-distance mechanotransduction in cells; however, a quantitative understanding of the dynamics of this transmission and the physical factors governing it remains lacking. Two key features of the actin cytoskeleton are its viscoelastic nature and the presence of prestress due to actomyosin motor activity. We develop a model of mechanical signal transmission through prestressed viscoelastic actin stress fibers that directly connect the cell surface to the nucleus. The analysis considers both temporally stationary and oscillatory mechanical signals and accounts for cytosolic drag on the stress fibers. To elucidate the physical parameters that govern mechanical signal transmission, we initially focus on the highly simplified case of a single stress fiber. The results demonstrate that the dynamics of mechanical signal transmission depend on whether the applied force leads to transverse or axial motion of the stress fiber. For transverse motion, mechanical signal transmission is dominated by prestress while fiber elasticity has a negligible effect. Conversely, signal transmission for axial motion is mediated uniquely by elasticity due to the absence of a prestress restoring force. Mechanical signal transmission is significantly delayed by stress fiber material viscosity, while cytosolic damping becomes important only for longer stress fibers. Only transverse motion yields the rapid and long-distance mechanical signal transmission dynamics observed experimentally. For simple networks of stress fibers, mechanical signals are transmitted rapidly to the nucleus when the fibers are oriented largely orthogonal to the applied force, whereas the presence of fibers parallel to the applied force slows down mechanical signal transmission significantly. The present results suggest that cytoskeletal prestress mediates rapid mechanical signal transmission and allows temporally oscillatory signals in the physiological frequency range to travel a long distance without significant decay due to material viscosity and/or cytosolic drag.
Bacterial Pathogens Associated with Community acquired Pneumonia : Authors Reply.

2. The use of oropharyngeal aspirate as the sample for isolation of bacterial pathogens associated with community acquired pneumonia (CAP) raises many questions. This is again highlighted by the isolation of organism like Acinetobacter and Citrobacter species from CAP cases. The value of isolating bacterial organisms that are frequently detected in the upper airways of children (eg, Streptococcus pneumoniae, Haemophilus influenzae, Staphylococcus aureus) are questionable. Nevertheless, had the authors provided the serotypes of the pneumococcal isolates, the presence of serotypes that are rarely found in the upper respiratory tract but are well recognized causes of invasive disease (eg, serotype 1), may have been highly predictive of pneumococcal pneumonia [2].
A metric model of amino acid substitution

MOTIVATION We address the question of whether there exists an effective evolutionary model of amino-acid substitution that forms a metric-distance function. There is always a trade-off between speed and sensitivity among competing computational methods of determining sequence homology. A metric model of evolution is a prerequisite for the development of an entire class of fast sequence analysis algorithms that are both scalable, O(log n) and sensitive. RESULTS We have reworked the mathematics of the point accepted mutation model (PAM) by calculating the expected time between accepted mutations in lieu of calculating log-odds probabilities. The resulting substitution matrix (mPAM) forms a metric. We validate the application of the mPAM evolutionary model for sequence homology by executing sequence queries from a controlled yeast protein homology search benchmark. We compare the accuracy of the results of mPAM and PAM similarity matrices as well as three prior metric models. The experiment shows that mPAM significantly outperforms the other three metrics and sufficiently approaches the sensitivity of PAM250 to make it applicable to the management of protein sequence databases.
Relation between neuropsychological impairment and functional disability in patients with chronic fatigue syndrome

OBJECTIVES To examine the relation between neuropsychological impairment and functional disability in patients with chronic fatigue syndrome, and determine whether the relation is independent of psychiatric factors. METHODS The subjects were 53 patients with chronic fatigue syndrome and 32 healthy controls who did not exercise regularly. Subjects were administered a structured psychiatric interview and completed questionnaires focusing on depression and functional disability. They also completed a battery of standardised neuropsychological tasks focusing on the cognitive domains that patients with chronic fatigue syndrome experience as particularly difficult: memory (verbal and visual), and attention/concentration. A test score was defined as failing when it was ⩾2 SD below the mean of the healthy controls after controlling for demographic factors. RESULTS Those patients with chronic fatigue syndrome with higher numbers of failing neuropsychological test scores reported significantly more days of general inactivity in the past month than those with fewer failing scores. This result remained significant even after partialling out the contribution of the presence of a comorbid axis I psychiatric episode and the overall level of depressive symptomology. Patients with failing verbal memory scores were particularly functionally disabled compared with those with passing scores. CONCLUSION A relation was found between cognitive impairment and functional disability which could not be explained entirely on the basis of psychiatric factors.
A Configurable, Extensible Implementation of Inter-Partition Communication for Integrated Modular Avionics

Aerial vehicles consist of many electronic devices connected through various networks. Thus, we should be able to describe them very clearly and easily to configure network channels. It is also highly desirable to have a framework that allows adding new network devices or protocols to the existing systems while minimizing the effects on the existing software. At the same time, since there are several kinds of network protocols available, an abstraction that supports multiple protocols in a transparent manner are essential to provide the portability of avionics applications. To address these, we extend the XML-based configuration of ARINC 653 so that the description of network devices and protocols can be done very systematically. In addition, we introduce the network manager that provides a transparent abstraction over multiple networks and efficient way of adding a new network protocol without modifications of existing software. We implement our design over Ethernet, Control Area Network (CAN) and POSIX Inter-Process Communication (IPC), and show its performance in terms of communication latency and jitter.
TRANSLATION IS NOT ENOUGH

ED INLINE CODES Inline codes, such as markers for bold or italics, links information or image references, can be represented using either an encapsulation mechanism or a placeholder method. Those are derived respectively from TMX and OpenTag. The encapsulation mechanism consists of bracketing the inline codes between special elements. XLIFF keeps a syntax very close to TMX: <bpt> (begin paired-tag); <ept> (end paired-tag); <it> (isolated tag); and <ph> (placeholder tag). If some text exists within a span of encapsulated code, it can be delimited by a <sub> element if the tool does not extract it as a separate segment, which would be the best solution. The placeholder method consists of extracting the inline codes out to the skeleton file and replacing them with placeholders to indicate their locations. The <g> element is the placeholder equivalent of <ept> and its ending tag </g> the equivalent of <bpt>. The elements <ex/> and <bx/> allow for the handling of overlapping inline codes; and the <x/> element is the equivalent of <ph>. Here is an example of inline tagging with code portions underlined: Click <bpt id='1'>&lt;a href="start.htm"> </bpt>here<ept id='1'>&lt;/a></ept> to
Constructive evaluation: a pedagogy of student-contributed assessment

We present an innovative pedagogical approach that we call constructive evaluation, which shifts students from being consumers of knowledge to participants in a community of peers engaged in actively producing and sharing knowledge. Students are required to author a question that assesses one or more of the learning outcomes of a course. In addition to the question, students write a sample solution. These questions and solutions are stored in a question item bank where they become available for other students to use as a learning resource. Once a student answers a question from the item bank, they can see how other students have answered the question and can reflect on their own response. Additionally, students must review the questions they have answered and are given an opportunity to engage in discussion of questions or answers via a feedback mechanism. In addition to improving content knowledge, students develop important meta-skills such as organising and communicating knowledge; judging the quality of information; giving and receiving feedback and improving self-assessment skills. This approach is aligned with both reflective professional practice and social theories of learning.
An Autopsy of the U.S. Financial System: Accident, Suicide, or Negligent Homicide?

Purpose - The purpose of this postmortem is to assess whether the design, implementation, and maintenance of financial policies during the period from 1996 through 2006 were primary causes of the financial system's demise. Design/methodology/approach - To draw conclusions about the policy determinants of the crisis, the paper studies five important policies: Securities and Exchange Commission (SEC) policies toward credit rating agencies, Federal Reserve policies concerning bank capital and credit default swaps, SEC and Federal Reserve policies about over-the-counter derivatives, SEC policies toward the consolidated supervision of major investment banks, and government policies toward two housing-finance entities, Fannie Mae and Freddie Mac. Findings - The evidence is inconsistent with the view that the collapse of the financial system was caused only by the popping of the housing bubble (“accident”) and the herding behavior of financiers rushing to create and market increasingly complex and questionable financial products (“suicide”). Rather, the evidence indicates that senior policymakers repeatedly designed, implemented, and maintained policies that destabilized the global financial system in the decade before the crisis. Moreover, although the major regulatory agencies were aware of the growing fragility of the financial system due to their policies, they chose not to modify those policies, suggesting that “negligent homicide” contributed to the financial system's collapse. Originality/value - Although influential policymakers presume that international capital flows, euphoric traders, and insufficient regulatory power caused the crisis, this paper shows that these factors played only a partial role. Thus, current reforms represent only a partial and thus incomplete step in establishing a stable and well-functioning financial system. Since systemic institutional failures helped cause the crisis, systemic institutional reforms must be a part of a comprehensively effective response.
Development of glycine- and GABA-gated currents in rat spinal motoneurons.

1. Developmental changes in glycine- and gamma-aminobutyric acid (GABA)-activated currents were studied in spinal motoneurons of embryonic and neonatal rats with the use of whole cell recording techniques. 2. Pressure ejection of glycine or GABA onto motoneuron somata produced Cl(-)-mediated inward currents and membrane depolarizations. During embryonic development, the average amplitude of GABA-gated currents was threefold larger than that of glycine-gated currents, but as a result of a large eightfold postnatal increase in glycine-activated currents, similar currents were produced by both amino acids after birth. 3. At all ages the decay of glycine- and GABA-gated currents best fit one-exponential curve, and their time constants were similar. The average decay time constant decreased by twofold after birth. 4. The ionic specificity of glycine- and GABA-gated channels was studied to determine whether the large amplitude of GABA-activated currents in embryonic motoneurons resulted from the contribution of an outward HCO-3 movement. Manipulations of Cl- and HCO-3 concentrations produced changes in the reversal potentials of glycine and GABA that were similar to the calculated changes in the equilibrium potentials of Cl-. This suggested that glycine- and GABA-gated currents were Cl- specific, and HCO-3 movement did not contribute more to the current generated by GABA than that produced by glycine. 5. Glycine- and GABA-gated currents were associated with severalfold increases in membrane conductance. The conductance increase generated by GABA in embryonic motoneurons was sevenfold larger than that generated by glycine, but similar conductance changes were produced by both amino acids after birth. (ABSTRACT TRUNCATED AT 250 WORDS)
LCB 03-0110, a Novel Pan-Discoidin Domain Receptor/c-Src Family Tyrosine Kinase Inhibitor, Suppresses Scar Formation by Inhibiting Fibroblast and Macrophage Activation

Wound healing generally induces an inflammatory response associated with tissue fibrosis in which activated macrophage and myofibroblast cells are primarily involved. Although this is known to be the underlying mechanism for scarring and various fibrotic pathologies, no effective intervention is currently available. We identified (3-(2-(3-(morpholinomethyl)phenyl)thieno[3,2-b]pyridin-7-ylamino)phenol (LCB 03-0110), a thienopyridine derivative, as a potent inhibitor of discoidin domain receptor family tyrosine kinases and discovered that this compound strongly inhibits several tyrosine kinases, including the c-Src family, spleen tyrosine kinase, Bruton's tyrosine kinase, and vascular endothelial growth factor receptor 2, which are important for immune cell signaling and inflammatory reactions. LCB 03-0110 suppressed the proliferation and migration of primary dermal fibroblasts induced by transforming growth factor β1 and type I collagen, and this result correlated with the inhibition ability of the compound against enhanced expression of α-smooth muscle actin and activation of Akt1 and focal adhesion kinase. In J774A.1 macrophage cells activated by lipopolysaccharide LCB 03-0110 inhibited cell migration and nitric oxide, inducible nitric-oxide synthase, cyclooxygenase 2, and tumor necrosis factor-α synthesis. LCB 03-0110 applied topically to full excisional wounds on rabbit ears suppressed the accumulation of myofibroblast and macrophage cells in the healing wound and reduced hypertrophic scar formation after wound closing, without delaying the wound closing process. Taken together, the pharmacological activities of LCB 03-0110 suggest that it could be an effective agent for suppressing fibroinflammation by simultaneously targeting activated fibroblasts and macrophages.
A Taxonomy of Distributed Storage Systems

Revision : 1.148 This paper presents a taxonomy of key topi s e e ting resear h and development of distributed storage systems. The taxonomy nds distributed storage systems to o er a wide array of fun tionality, employ ar hite tures with varying degrees of entralisation and operate a ross environments with varying trust and s alability. Furthermore, taxonomies on autonomi management, federation, onsisten y and routing provide an insight into hallenges fa ed by distributed storage systems and the resear h to over ome them. The paper ontinues by providing a survey of distributed storage systems whi h exemplify topi s overed in the taxonomy. The sele tion of surveyed systems overs a variety of storage systems, exposing the reader to an array of di erent problems and solutions employed to over ome these hallenges. For ea h surveyed system we address the underlying operational behaviour, leading into the ar hite ture and algorithms employed in the design and development of the system. Our survey overs systems from the past and present on luding with a dis ussion on the evolution of distributed storage systems and possible future work.
Cirsium candelabrum Griseb. (Asteraceae) in Croatia - the beginning of its invasive spread outside natural range?

The natural range of a species Cirsium candelabrum Griseb. (Asteraceae) comprises the territory of the Balkans (Balkan endemic): Bosnia and Herzegovina, Montenegro, Albania, Serbia, Kosovo, Macedonia, Greece, Bulgaria and south-west Romania. Outside of its natural range, C. candelabrum has recently been found in the European part of Turkey, in Slovenia and Croatia. First findings in Croatia were reported from south Croatian region of Dalmatia in 2008 and 2010 by Jasenka Topic. The species was included, based on these findings, in „Flora Croatica“ Database in 2008. In summer 2014, we were looking for the localities of C. candelabrum in Dalmatia, from the hinterland of cities of Split and Makarska to the border area between Croatia and Bosnia and Herzegovina. A large number of new localities (50) was found, mainly on industrial zone of Dugopolje and along the roads leading towards border crossings of settlements of Aržano and Kamensko. The results indicate the spread of this plant in the hinterland of Dalmatia from Bosnia and Herzegovina. The plant grows in ruderal habitats along roads, especially when the natural vegetation has been removed by means of road building or reconstruction. Monitoring can help us to understand whether the latest findings of C. candelabrum on localities outside its natural range is only a temporary phenomenon or is it the beginning of its invasive spread. So far, it occurs only on anthropogenic habitats and shows no tendency to spread on agricultural land or natural habitats and vegetation.
Mechanisms and policies for supporting fine-grained cycle stealing

This paper presents an investigation into local mechanisms and scheduling policies that allow guest processes to efficiently exploit otherwise-idle workstation resources. Unlike traditional policies that harvest cycles only from unused machines, we target policies that exploit resources even from machines that have active users. We present a set of kernel extensions that allow these policies to operate without significantly impacting host processes: 1) a new guest process priority that prevents processes from stealing any processor time from host processes, 2) a new page replacement policy that imposes hard bounds on the number of physical pages that can be obtained by guest processes when host processes are active, and 3) a new page-out strategy that adaptively increases the pageout rate of guest processes when new host processes are started.
Regulatory T cells suppress antigen‐driven CD4 T cell reactivity following injury

Injury initiates local and systemic host responses and is known to increase CD4 Treg activity in mice and humans. This study uses a TCR transgenic T cell adoptive transfer approach and in vivo Treg depletion to determine specifically the in vivo influence of Tregs on antigen‐driven CD4 T cell reactivity following burn injury in mice. We report here that injury in the absence of recipient and donor Tregs promotes high antigen‐driven CD4 T cell expansion and increases the level of CD4 T cell reactivity. In contrast, CD4 T cell expansion and reactivity were suppressed significantly in injured Treg‐replete mice. In additional experiments, we found that APCs prepared from burn‐ or sham‐injured, Treg‐depleted mice displayed significantly higher antigen‐presenting activity than APCs prepared from normal mice, suggesting that Tregs may suppress injury responses by controlling the intensity of APC activity. Taken together, these findings demonstrate that Tregs can actively control the in vivo expansion and reactivity of antigen‐stimulated, naïve CD4 T cells following severe injury.