Miracle-dz/UniFAR-FTUs huggingface dataset:
Solving Hierarchical Constraints over Finite Domains

Many real world problems have requirements and constraints which con ict with each other and are not well de ned. One framework for dealing with such over-constrained/fuzzy problems is provided by constraint hierarchies, where constraints are divided into ranks, and where a comparator selects preferred solutions over others. In this paper, we present a framework for formulating hierarchical constraint problems over nite domains (HCPs). We show, how the recent framework of over-constrained integer programs (OIPs) can be extended to handle non-linear constraints and to exploit constraint hierarchies. The motivation for this work arose from solving large airport gate allocation problems. We show how gate allocation problems can be formulated as HCPs using typical gate allocation constraints. Using gate allocation benchmarks with varying problem characteristics, we compare local search on the given HCPs with local search and integer programming on linear reformulations of the HCPs.
Plasmids from Food Lactic Acid Bacteria: Diversity, Similarity, and New Developments

Plasmids are widely distributed in different sources of lactic acid bacteria (LAB) as self-replicating extrachromosomal genetic materials, and have received considerable attention due to their close relationship with many important functions as well as some industrially relevant characteristics of the LAB species. They are interesting with regard to the development of food-grade cloning vectors. This review summarizes new developments in the area of lactic acid bacteria plasmids and aims to provide up to date information that can be used in related future research.
Outcome of Symptomatic Intracranial Atherosclerotic Disease

Background and Purpose— Patients with intracranial atherosclerotic disease have a 3.6% to 22% annual risk of stroke. In this study, we sought to evaluate the natural history and prognosis of patients with symptomatic intracranial atherosclerotic disease who received medical therapy versus percutaneous transluminal angioplasty and stenting (PTAS) at our institution. Methods— Charts of all patients with symptomatic intracranial atherosclerotic disease from July 2004 to September 2007 were reviewed and assessed for history of transient ischemic attack or stroke. Patients were either treated with “best medical therapy” (Medical Therapy Group) or PTAS plus antiplatelet agents (PTAS Group) and followed prospectively. A favorable outcome was defined as the absence of transient ischemic attacks, strokes, or vascular death; modified Rankin Scale of ≤3; and no endovascular reintervention of symptomatic in-stent restenosis. Results— One hundred eleven patients fulfilled entry criteria, with 58 (52.3%) and 53 patients (47.7%) enrolled in the Medical Therapy and PTAS Groups, respectively. Thirty-eight patients of the Medical Therapy Group (65.5%) had a favorable outcome compared with 37 patients of the PTAS Group (69.8%). Combined ischemic end point data for the occurrence of transient ischemic attack, stroke, and vascular death was similar with 14 (24%) events in the Medical Therapy Group versus 15 (28.3%) events in the PTAS Group. Conclusion— Overall, the combined ischemic end point was the same in the Medical Therapy and PTAS Groups.
How Firms Respond to Mandatory Information Disclosure

Mandatory information disclosure regulations seek to create institutional pressure to spur performance improvement. By examining how organizational characteristics moderate establishments' responses to a prominent environmental information disclosure program, we provide among the first empirical evidence characterizing heterogeneous responses by those mandated to disclose information. We find particularly rapid improvement among establishments located close to their headquarters and among establishments with proximate siblings, especially when the proximate siblings are in the same industry. Large establishments improve more slowly than small establishments in sparse regions, but both groups improve similarly in dense regions, suggesting that density mitigates the power of large establishments to resist institutional pressures. Finally, privately held firms' establishments outperform those owned by public firms. We highlight implications for institutional theory, managers, and policymakers.
The Neutral Hydrogen Distribution in Merging Galaxies: Differences between Stellar and Gaseous Tidal Morphologies

As part of several H I synthesis-mapping studies of merging galaxies, we have mapped the tidal gas in the three disk-disk merger systems Arp 157 (NGC 520), Arp 220, and Arp 299 (NGC 3690). These systems differ from the majority of the mergers mapped in H I in that their stellar and gaseous tidal features do not coincide. In particular, they exhibit large stellar tidal features with little if any accompanying neutral gas and large gas-rich tidal features with little if any accompanying starlight. On smaller scales, there are striking anticorrelations in which the gaseous and stellar tidal features appear to cross. We explore several possible causes for these differences, including dust obscuration, ram pressure stripping, and ionization effects. No single explanation can account for all of the observed differences. The fact that each of these systems shows evidence for a starburst-driven superwind expanding in the direction of the most striking anticorrelations leads us to suggest that the superwind is primarily responsible for the observed differences, either by sweeping the features clear of gas via ram pressure or by excavating a clear sightline toward the starburst and allowing UV photons to ionize regions of the tails. If this suggestion is correct, only systems hosting a galactic superwind and experiencing a high-inclination encounter geometry (such that tidal gas is lifted high above the starburst regions) should exhibit such extreme differences between their H I and optical tidal morphologies.
Fully Secure Codes Based Tracing and Revoking Scheme with Constant Ciphertext

In broadcast encryption system certain users may leak their decryption keys to build pirate decoders, so traitor tracing is quite necessary. There exist many codes based traitor tracing schemes. As pointed out by Billet and Phan in ICITS 2008, these schemes lack revocation ability. The ability of revocation can disable identified malicious users and users who fail to fulfill the payments, so that the broadcast encryption system can be more practical. Recently, Zhao and Li presented a construction of codes based tracing and revoking scheme which achieves user revocation as well as traitor tracing. However, their scheme is only secure against chosen plaintext attacks under selective-adversary model with random oracle. In this paper, we obtain a new construction of codes based tracing and revoking scheme which is proved secure against chosen ciphertext attacks under adaptive-adversary model without random oracle. Our idea is to insert codeword into Boneh and Hamburgs identity based broadcast encryption scheme to retain the ability of user revocation and use Boneh and Naors method to trace traitors. Our fully secure scheme is roughly as efficient as Zhao and Lis scheme while the security is enhanced.
Impact of Forming, Welding, and Electropolishing on Pitting and the Surface Finish of SRF Cavity Niobium

A broad range of coupon electropolishing experiments are described to ascertain the mechanism(s) by which large defects are formed near superconducting radio-frequency (SRF) cavity welds. Cold-worked vs. annealed metal, the presence of a weld, and several variations of electropolishing (EP) parameters were considered. Pitting is strongly promoted by cold work and agitation of the EP solution. Welding also promotes pitting, but less so compared with the other factors above. Temperature increase during EP did not strongly affect glossiness or pitting, but the reduced viscosity made the electrolyte more susceptible to agitation. The experiments suggest that several factors that are rather benign alone are combined by the cavity forming, welding, and processing sequence to promote the formation of defects such as pits. Process changes to mitigate these risks are discussed.
Spectral Tuning, Fluorescence, and Photoactivity in Hybrids of Photoactive Yellow Protein, Reconstituted with Native or Modified Chromophores*

Photoactive yellow proteins (PYPs) constitute a new class of eubacterial photoreceptors, containing a deprotonated thiol ester-linked 4-hydroxycinnamic acid chromophore. Interactions with the protein dramatically change the (photo)chemical properties of this cofactor. Here we describe the reconstitution of apoPYP with anhydrides of various chromophore analogues. The resulting hybrid PYPs, their acid-denatured states, and corresponding model compounds were characterized with respect to their absorption spectrum, pK for chromophore deprotonation, fluorescence quantum yield, and Stokes shift. Three factors contributing to the tuning of the absorption of the hybrid PYPs were quantified: (i) thiol ester bond formation, (ii) chromophore deprotonation, and (iii) specific chromophore-protein interactions. Analogues lacking the 4-hydroxy substituent lack both contributions (chromophore deprotonation and specific chromophore-protein interactions), confirming the importance of this substituent in optical tuning of PYP. Hydroxy and methoxy substituents in the 3- and/or 5-position do not disrupt strong interactions with the protein but increase their pK for protonation and the fluorescence quantum yield. Both deprotonation and binding to apoPYP strongly decrease the Stokes shift of chromophore fluorescence. Therefore, coupling of the chromophore to the apoprotein not only reduces the energy gap between its ground and excited state but also the extent of reorganization between these two states. Two of the PYP hybrids show photoactivity comparable with native PYP, although with retarded recovery of the initial state.
A polynomial time approximation scheme for minimum routing cost spanning trees

Given an undirected graph with nonnegative costs on the edges, the routing cost of any of its spanning trees is the sum over all pairs of vertices of the cost of the path between the pair in the tree. Finding a spanning tree of minimum routing cost is NP-hard, even when the costs obey the triangle inequality. We show that the general case is in fact reducible to the metric case and present a polynomial-time approximation scheme valid for both versions of the problem. In particular, we show how to build a spanning tree of an n-vertex weighted graph with routing cost at most $(1+\epsilon)$ of the minimum in time $O(n^{O({\frac{1}{\epsilon}}% )})$. Besides the obvious connection to network design, trees with small routing cost also find application in the construction of good multiple sequence alignments in computational biology. The communication cost spanning tree problem is a generalization of the minimum routing cost tree problem where the routing costs of different pairs are weighted by different requirement amounts. We observe that a randomized O(log n log log n)-approximation for this problem follows directly from a recent result of Bartal, where n is the number of nodes in a metric graph. This also yields the same approximation for the generalized sum-of-pairs alignment problem in computational biology.
High Dynamic Range Imaging

High dynamic range (HDR) images and video contain pixels, which can represent much greater range of colors and brightness levels than that offered by existing, standard dynamic range images. Such “better pixels” greatly improve the overall quality of visual content, making it appear much more realistic and appealing to the audience. HDR is one of the key technologies of the future imaging pipeline, which will change the way the digital visual content is represented and manipulated. This article offers a broad review of the HDR methods and technologies with an introduction to fundamental concepts behind the perception of HDR imagery. It serves as both an introduction to the subject and a review of the current state of the art in HDR imaging. It covers the topics related to capture of HDR content with cameras and its generation with computer graphics methods; encoding and compression of HDR images and video; tone mapping for displaying HDR content on standard dynamic range displays; inverse tone mapping for upscaling legacy content for presentation on HDR displays; the display technologies offering HDR range; and finally image and video quality metrics suitable for HDR content. Keywords: high dynamic range imaging; tone mapping
Epidemiology of Acute Respiratory Infections in Children in Guangzhou: A Three-Year Study

Acute Respiratory Infections (ARI) are some of the most common human diseases worldwide. However, they have a complex and diverse etiology, and the characteristics of the pathogens involved in respiratory infections in developing countries are not well understood. In this work, we analyzed the characteristics of 17 common respiratory pathogens in children (≤14 years old) with ARI in Guangzhou, southern China over a 3-year period using real-time polymerase chain reaction. Pathogens were identified in 2361/4242 (55.7%) patients, and the positivity rate varied seasonally. Ten of the 17 pathogens investigated showed positivity rates of more than 5%. The most frequently detected pathogens were respiratory syncytial virus (768/2361, 32.5%), influenza A virus (428/2361, 18.1%), enterovirus (138/2361, 13.3%), Mycoplasma pneumoniae (267/2361, 11.3%) and adenovirus (213/2361, 9.0%). Co-pathogens were common and found in 503 of 2361 (21.3%) positive samples. When ranked according to frequency of occurrence, the pattern of co-pathogens was similar to that of the primary pathogens, with the exception of human bocavirus, human coronavirus and human metapneumovirus. Significant differences were found in age prevalence in 10 of the 17 pathogens (p≤0.009): four basic patterns were observed, A: detection rates increased with age, B: detection rates declined with age, C: the detection rate showed distinct peaks or D: numbers of patients were too low to detect a trend or showed no significant difference among age groups (p>0.05). These data will be useful for planning vaccine research and control strategies and for studies predicting pathogen prevalence.
Stress-induced selective nano-crystallization in laser-processed amorphous Fe–Si–B alloys

It is shown that laser processing results in localized compressive stresses in amorphous Fe–Si–B, leading to homogeneous nano-crystallization at the edges of the laser track. The mechanism can be attributed to enhanced diffusivity at these edges, resulting from a reduced diffusion activation barrier, which has been calculated by coupling the results of a thermal model with microstructural characterization.
Characteristics and Outcomes of Patients With Goodpasture's Syndrome

Background. Goodpasture's syndrome is a rare disorder characterized by pulmonary hemorrhage, glomerulonephritis, and antiglomerular basement membrane antibodies. Methods. Case reports of Goodpasture's syndrome between 1993 and 2000 were identified using MEDLINE. Each case was reviewed for clinical manifestations, laboratory features, pathophysiology, treatment options, and outcomes. Results. Eighty-five cases of Goodpasture's syndrome were reported in the English language literature. The mean age of patients in this review was 44 years. Most patients had multiple risk factors. Smoking was strongly associated with pulmonary hemorrhage. Most patients presented with hemoptysis and crackles. More than 90% had antiglomerular basement membrane antibodies, and 80% had crescenteric glomerulonephritis on renal biopsy. Conclusion. Most patients were treated with immunosuppression and plasma exchange and were alive at follow-up. Patients with either pulmonary or renal signs and symptoms should be evaluated for Goodpasture's syndrome, since early diagnosis allows prompt treatment and improved outcome.
Progress in the diagnosis and management of aspergillosis in bone marrow transplantation: 13 years' experience.

Over 13 years, we have seen 16 cases of proven invasive aspergillosis in 446 bone marrow transplant recipients, an incidence of 3.6%. The incidence of infection is low in patients with uncomplicated allogeneic or autologous bone-marrow transplants (< 2% and 0, respectively). Of the 16 episodes following transplantation, 10 occurred in patients with late transplant complications who were no longer in protective isolation. In patients who had focal pulmonary lesions (as diagnosed by computed tomographic scanning), culture of bronchoalveolar lavage (BAL) fluid was not an effective diagnostic procedure. In diffuse pulmonary disease due to Aspergillus, culture of BAL fluid had a sensitivity of 100%. Aspergillus species were isolated from an additional six patients who had no evidence of invasive aspergillosis. Graft rejection was a significant predisposing factor for the development of invasive aspergillosis (P < .001, log-rank test), and in our hospital, these patients now receive intravenous amphotericin B as prophylaxis. None of the six patients whose chest roentgenograms showed abnormalities before transplantation and who underwent surgical resection as part of the treatment for invasive aspergillosis developed recurrent infection.
= 4 gauged supergravity from duality-twist compactifications of string theory

We investigate the lifting of half-maximal four-dimensional gauged supergravities to compactifications of string theory. It is shown that a class of such supergravities can arise from compactifications of IIA string theory on manifolds of SU(2)-structure which may be thought of as K3 fibrations over T2. Examples of these SU(2)-structure backgrounds, as smooth K3 bundles and as compactifications with H-flux, are given and we also find evidence for a class of non-geometric, Mirror-fold backgrounds. By applying the duality between IIA string theory on K3 and Heterotic string theory on T4 fibrewise, we argue that these SU(2)-structure backgrounds are dual to Heterotic compactifications on a class T4 fibrations over T2. Examples of these fibrations as twisted tori, H-flux and T-fold compactifications are given. We also construct a new set of backgrounds, particular to Heterotic string theory, which includes a previously unknown class of Heterotic T-folds. A sigma model description of these backgrounds, from the Heterotic perspective, is presented in which we generalize the Bosonic doubled formalism to Heterotic string theory.
Genetics of individual differences in bitter taste perception: lessons from the PTC gene

The ability or inability to taste the compound phenylthiocarbamide (PTC) is a classic inherited trait in humans and has been the subject of genetic and anthropological studies for over 70 years. This trait has also been shown to correlate with a number of dietary preferences and thus may have important implications for human health. The recent identification of the gene that underlies this phenotype has produced several surprising findings. This gene is a member of the T2R family of bitter taste receptor genes. It exists in seven different allelic forms, although only two of these, designated the major taster and major non‐taster forms, exist at high frequency outside sub‐Saharan Africa. The non‐taster allele resides on a small chromosomal region identical by descent, indicating that non‐tasters are descended from an ancient founder individual, and consistent with an origin of the non‐taster allele preceding the emergence of modern humans out of Africa. The two major forms differ from each other at three amino acid positions, and both alleles have been maintained at high frequency by balancing natural selection, suggesting that the non‐taster allele serves some function. We hypothesize that this function is to serve as a receptor for another, as yet unidentified toxic bitter substance. At least some of the remaining five haplotypes appear to confer intermediate sensitivity to PTC, suggesting future detailed studies of the relationships between receptor structure and taste function.
Population pharmacokinetics of sevoflurane in conjunction with the AnaConDa®: toward target‐controlled infusion of volatiles into the breathing system

Background: The Anesthetic Conserving Device (AnaConDa®) uncouples delivery of a volatile anesthetic (VA) from fresh gas flow (FGF) using a continuous infusion of liquid volatile into a modified heat–moisture exchanger capable of adsorbing VA during expiration and releasing adsorbed VA during inspiration. It combines the simplicity and responsiveness of high FGF with low agent expenditures. We performed in vitro characterization of the device before developing a population pharmacokinetic model for sevoflurane administration with the AnaConDa®, and retrospectively testing its performance (internal validation).
LiveBench‐1: Continuous benchmarking of protein structure prediction servers

We present a novel, continuous approach aimed at the large‐scale assessment of the performance of available fold‐recognition servers. Six popular servers were investigated: PDB‐Blast, FFAS, T98‐lib, GenTHREADER, 3D‐PSSM, and INBGU. The assessment was conducted using as prediction targets a large number of selected protein structures released from October 1999 to April 2000. A target was selected if its sequence showed no significant similarity to any of the proteins previously available in the structural database. Overall, the servers were able to produce structurally similar models for one‐half of the targets, but significantly accurate sequence‐structure alignments were produced for only one‐third of the targets. We further classified the targets into two sets: easy and hard. We found that all servers were able to find the correct answer for the vast majority of the easy targets if a structurally similar fold was present in the server's fold libraries. However, among the hard targets—where standard methods such as PSI‐BLAST fail—the most sensitive fold‐recognition servers were able to produce similar models for only 40% of the cases, half of which had a significantly accurate sequence‐structure alignment. Among the hard targets, the presence of updated libraries appeared to be less critical for the ranking. An “ideally combined consensus” prediction, where the results of all servers are considered, would increase the percentage of correct assignments by 50%. Each server had a number of cases with a correct assignment, where the assignments of all the other servers were wrong. This emphasizes the benefits of considering more than one server in difficult prediction tasks. The LiveBench program (http://BioInfo.PL/LiveBench) is being continued, and all interested developers are cordially invited to join.
On two-door three-dimensional container packing problem under home delivery service

This paper considers the three-dimensional container packing problem (3DCPP) under home delivery service, which predetermines an ordering of delivering ordered cargo boxes to customers, and aims to load a subset of those boxes according to the delivery ordering into a 3D car container with maximal utilization ratio of the container space while prohibiting the process of delivering cargos to each customer from unloading and subsequent reloading of boxes. In practice, cargos can be taken out from not only the rear door of the delivery container but also the side door. Nonetheless, the previous research only considered the case with only a single door. Therefore, this paper establishes the model for the two-door 3DCPP under home delivery service. Furthermore, the rule of invisible and untouchable items and the subvolume-based approach for the one-door problem are extended to resolve the two-door problem. Last, simulation analysis verifies performance of our approach.