Miracle-dz/UniFAR-FTUs huggingface dataset:
αvβ3-dependent cross-presentation of matrix metalloproteinase–2 by melanoma cells gives rise to a new tumor antigen

A large array of antigens that are recognized by tumor-specific T cells has been identified and shown to be generated through various processes. We describe a new mechanism underlying T cell recognition of melanoma cells, which involves the generation of a major histocompatibility complex class I–restricted epitope after tumor-mediated uptake and processing of an extracellular protein—a process referred to as cross-presentation—which is believed to be restricted to immune cells. We show that melanoma cells cross-present, in an αvβ3-dependent manner, an antigen derived from secreted matrix metalloproteinase–2 (MMP-2) to human leukocyte antigen A*0201-restricted T cells. Because MMP-2 activity is critical for melanoma progression, the MMP-2 peptide should be cross-presented by most progressing melanomas and represents a unique antigen for vaccine therapy of these tumors.
Obsessional Cliques: A Semantic Characterization of Bounded Time Complexity

We give a semantic characterization of bounded complexity proofs. We introduce the notion of obsessional clique in the relational model of linear logic and show that restricting the morphisms of the category RscrEscrLscr to obsessional cliques yields models of ELL and SLL. Conversely, we prove that these models are relatively complete: an LL proof whose interpretation is an obsessional clique is always an ELL/SLL proof. These results are achieved by introducing a system of ELL/SLL untyped proof-nets, which is both correct and complete with respect to elementary/polynomial time complexity
Does Donor Brain Death Influence Acute Vascular Rejection in the Kidney Transplant?

Background. There is increasing experimental evidence to suggest that donor brain death enhances susceptibility to early inflammatory responses such as acute rejection in the kidney transplant. The aim of the present study was to establish whether the injury induced or aggravated by donor brain death could exert an effect on recipient immunologic tolerance by comparing data from patients receiving a kidney from non–heart-beating donors (NHBD) or from brain-dead donors (BDD). Methods. We reviewed data corresponding to 372 renal transplants performed from January 1996 to May 2002. The data were stratified according to donor type as 197 (53%) brain-dead and 175 (47%) non–heart-beating donors, and the two groups were compared in terms of acute vascular rejection by Cox’s regression analysis. Results. The rate of vascular rejection was 28% in the BDD group and 21.7% in the NHBD (P=0.10). The following predictive variables for acute vascular rejection were established: brain death [RR 1.77 (95% CI 1.06–3.18)], presence of delayed graft function [RR 3.33 (1.99–5.55)], previous transplant [RR 2.35 (1.34–4.13)], recipient age under 60 years [RR 1.86 (0.99–2.28)], female recipient [RR 1.50 (0.99–2.28)], cerebrovascular disease as cause of donor death [RR 1.72 (1.02–2.91)], and triple therapy as immunosuppressive treatment. Conclusion. Donor brain death could be a risk factor for the development of vascular rejection in kidney recipients. This process could affect the quality of the graft and host alloresponsiveness. Delayed graft function in transplants from dead brain donors could be a reflection of severe autonomic storm, leading to a higher incidence of vascular rejection in these patients.
Analysis of a Tornadic Mesoscale Convective Vortex Based on Ensemble Kalman Filter Assimilation of CASA X-Band and WSR-88D Radar Data

AbstractOne of the goals of the National Science Foundation Engineering Research Center (ERC) for Collaborative Adaptive Sensing of the Atmosphere (CASA) is to improve storm-scale numerical weather prediction (NWP) by collecting data with a dense X-band radar network that provides high-resolution low-level coverage, and by assimilating such data into NWP models. During the first spring storm season after the deployment of four radars in the CASA Integrated Project-1 (IP-1) network in southwest Oklahoma, a tornadic mesoscale convective system (MCS) was captured by CASA and surrounding Weather Surveillance Radars-1988 Doppler (WSR-88Ds) on 8–9 May 2007. The MCS moved across northwest Texas and western and central Oklahoma; two tornadoes rated as category 1 on the enhanced Fujita scale (EF-1) and one tornado of EF-0 intensity were reported during the event, just to the north of the IP-1 network. This was the first tornadic convective system observed by CASA.To quantify the impacts of CASA radar data in storm.
Differential Cofactor Requirements for Histone Eviction from Two Nucleosomes at the Yeast PHO84 Promoter Are Determined by Intrinsic Nucleosome Stability

ABSTRACT We showed previously that the strong PHO5 promoter is less dependent on chromatin cofactors than the weaker coregulated PHO8 promoter. In this study we asked if chromatin remodeling at the even stronger PHO84 promoter was correspondingly less cofactor dependent. The repressed PHO84 promoter showed a short hypersensitive region that was flanked upstream and downstream by a positioned nucleosome and contained two transactivator Pho4 sites. Promoter induction generated an extensive hypersensitive and histone-depleted region, yielding two more Pho4 sites accessible. This remodeling was strictly Pho4 dependent, strongly dependent on the remodelers Snf2 and Ino80 and on the histone acetyltransferase Gcn5, and more weakly on the acetyltransferase Rtt109. Importantly, remodeling of each of the two positioned nucleosomes required Snf2 and Ino80 to different degrees. Only remodeling of the upstream nucleosome was strictly dependent on Snf2. Further, remodeling of the upstream nucleosome was more dependent on Ino80 than remodeling of the downstream nucleosome. Both nucleosomes differed in their intrinsic stabilities as predicted in silico and measured in vitro. The causal relationship between the different nucleosome stabilities and the different cofactor requirements was shown by introducing destabilizing mutations in vivo. Therefore, chromatin cofactor requirements were determined by intrinsic nucleosome stabilities rather than correlated to promoter strength.
Understanding temporal aspects in document classification

Due to the increasing amount of information present on the Web, Automatic Document Classification (ADC) has become an important research topic. ADC usually follows a standard supervised learning strategy, where we first build a model using preclassified documents and then use it to classify new unseen documents. One major challenge for ADC in many scenarios is that the characteristics of the documents and the classes to which they belong may change over time. However, most of the current techniques for ADC are applied without taking into account the temporal evolution of the collection of documents In this work, we perform a detailed study of the temporal evolution in the ADC, introducing an analysis methodology. We discuss that temporal evolution may be explained by three factors: 1) class distribution; 2) term distribution; and 3) class similarity. We employ metrics and experimental strategies capable of isolating each of these factors in order to analyze them separately, using two very different document collections: the ACM Digital Library and the Medline medical collections. Moreover, we present some preliminary results of potential gains that could be obtained by varying the training set to find the ideal size that minimizes the time effects. We show that by using just 69% of the ACM database, we are able to have an accuracy of 89.76%, and with only 25% of the Medline, an accuracy of 87.57%, which means gains of up to 20% in accuracy with much smaller training sets
Jena Research Papers in Business and Economics Cross Dock Scheduling: Classification, Literature Review and Research Agenda Cross Dock Scheduling: Classication, Literature Review and Research Agenda

At cross docking terminals incoming deliveries of inbound trucks are unloaded , sorted, moved across the dock and nally loaded onto outbound trucks, which immediately leave the terminal towards their next destination in the distribution chain. Accordingly, a cross dock is a consolidation point in a distribution network, where multiple smaller shipments can be merged to full truck loads in order to realize economies in transportation. In this context, the truck scheduling problem, which decides on the succession of truck processing at the dock doors, is especially important to ensure a rapid turnover and on-time deliveries. Due to its high real-world signicance, several truck scheduling procedures have been introduced within the recent years, which all treat specic cross dock settings. In order to structure and promote scientic progress, the paper on hand introduces a classication of deterministic truck scheduling. With the help of this classication, existing literature is reviewed and future research needs are identied. Moreover, we represent a yet unexplored class of truck scheduling problems which is highly relevant in real-world distribution networks.
BoX-MACs : Exploiting Physical and Link Layer Boundaries in Low-Power Networking

We present two MAC layers for ultra-low-power wireless networking, BoX-MAC-1 and BoX-MAC-2. Leading low-power MACs today reside in a single layer: BMAC exploits only the physical-layer while XMAC utilizes only the link-layer. In contrast, BoX-MAC-1 and BoX-MAC-2 are cross-layer protocols. BoX-MAC-1 incorporates link-layer information into a predominantly physical-layer sampling approach. BoX-MAC-2 combines physical-layer information into a predominantly link-layer packetized approach. Through analysis and experiments on CC2420-based platforms, we find these cross-layer protocols consume up to 40-50% less energy than XMAC and 30% less energy than BMAC under reasonable workloads. Furthermore, BoXMAC-2 yields up to 46% more throughput than its XMAC counterpart. Together, BoX-MAC protocols provide a comprehensive set of low-power link-layer primitives for a wide range of network workloads. The advantages of these crosslayer MAC designs over single-layer approaches provide insight on requirements for future radio chip and platform
Allergic transfusion reactions: an evaluation of 273 consecutive reactions.

CONTEXT Allergic reaction to transfusion is common. However, the review of a large series of allergic transfusion reactions has not been performed. OBJECTIVE To review a large series of allergic transfusion reactions. DESIGN A retrospective review of all reported and evaluated transfusion reactions during a 9-year period at 1 institution was performed. Associated clinical signs and symptoms were evaluated. SETTING Large, tertiary-care teaching hospital. RESULTS A total of 1613 adverse reactions to transfusion were evaluated. Allergic transfusion reactions accounted for 17% (273 of 1613) of the transfusion reactions. Severe allergic reactions (anaphylaxis, anaphylactoid signs and symptoms, and/or hypotension) were observed in 21 patients (7.7% of allergic reactions, or 1.3% of all transfusion reactions). Serum tryptase, a marker for anaphylaxis, was measured in 1 patient and determined to be borderline elevated. Five patients experienced allergic transfusion reactions to autologous red cell transfusions. One patient experienced hives during the transfusion of a major ABO mismatched red blood cell. A wide variety of skin manifestations were observed, but 26 (9.5%) patients did not have skin manifestations. Allergic transfusion reactions were estimated to occur in approximately 1 in 4124 blood components transfused, or 1 in 2338 transfusion episodes. Severe allergic reactions occurred in approximately 1 in 30,281 transfusions. No deaths directly attributable to transfusion were observed in this patient group. CONCLUSIONS The clinical presentation of allergic transfusion reactions was quite variable, and the pathophysiology remains unclear. Recommendations for clinical evaluation and therapy remain problematic and often empirical.
Changes in Atmospheric Butanes and Pentanes and Their Isomeric Ratios in the Continental United States

Nonmethane hydrocarbons have been used as tracers in research on emissions and atmospheric oxidation chemistry. This research investigates source region mixing ratio trends of the nonmethane hydrocarbons i‐butane, n‐butane, i‐pentane, and n‐pentane, and the (i/n) isomeric ratios of these compounds between 2001 and 2015. Data collected at Photochemical Assessment Monitoring Stations, mandated by the U.S. Environmental Protection Agency in ozone nonattainment areas, and data collected at Global Greenhouse Gas Reference Network sites within the National Oceanic and Atmospheric Administration network, and analyzed at the Institute of Arctic and Alpine Research at the University of Colorado‐Boulder, were examined. Among all considered species, linear regression analyses on concentration time series had negative slopes at 81% of sites, indicating predominantly declining butane and pentane atmospheric concentrations. Mostly negative slopes (78% of sites) were found for the (i/n) butane and pentane isomeric ratios, including all six and seven statistically significant (i/n) butane and pentane trends, respectively. Over the ~15 year investigation period and averaged over all sites, total relative changes were ~30 and 45% for the (i/n) ratios of butanes and pentanes, respectively, with a relative increase in the prominence of the n‐isomers. Most likely causes include changing isomeric ratios in gasoline sector emissions, and increasing influence of oil and natural gas industry emissions. Changes in concentrations and isomeric ratios depend on proximity of contributing emission sources to measurement sites.
Cognitive Development in Children With Language Impairment, and Correlation Between Language and Intelligence Development in Kindergarten Children With Developmental Delay

We performed a retrospective review of 65 children with developmental delay. The male-to-female ratio was 2.25 : 1, and the mean age was 5.8 years; performance IQ was 94.8, verbal IQ was 83, and full-scale IQ was 87.4. Twenty-three (35%) children had normal language development, 13 (20%) had below average language development, and 29 (45%) had developmental language disorder. Performance IQ was significantly better than verbal IQ in all children (P < .001), and there was no difference within the 3 language groups. The performance IQ (P = .007) of children with developmental language disorder and specific language impairment was significantly lower than that of children with normal language development. Performance IQ was found to be correlated with language score (r = .309, P = .012). The children with language impairment were associated with lower IQ scores. The discrepancy between performance IQ and verbal IQ persisted in children with developmental delay, not only in children with language disorder.
The Effects of Various Anti-G Suit Pressures and Positive Pressure Breathing on Lung Volumes as Measured by Spirometry at +1 Gz.

Abstract : Anti-G Suits have historically been evaluated using G-tolerance as the primary benchmark of a G-suit's effectiveness. One area which has been overlooked for over fifty years of G-suit design, is the effect of G-suit inflation on lung volumes. Lung inflation to about 75 percent of normal capacity is the key to producing the optimum intrathoracic pressure for performing the anti-G straining maneuver. This study evaluated three separate GH-suit designs, at +1 Gz and looked at the effect positive pressure breathing (PPB) had on maintaining lung volumes during G-suit inflations to 4, 6, and 8 psi. Lung volumes were measured using a microprocessor based spirometer. Results showed that the full pressure suit design (APS) had the smallest effect on inspiration. But in a comparison of the standard G-suit (trousers), the full coverage trousers (ATA0S) proved to be superior in design compared to the standard five bladder suit (CSU-13B/P). At suit pressures of 8 psi, Forced Inspiratory Vital Capacity (FIVC) percent change from baseline values for the APS, ATAGS, and CSU-13B/P were 80, 93, and 60% respectively. When PPB was added, FIVC values were 102, 66, and 46% respectively. These data show that the addition of PPB with anti-G suit trousers becomes a liability to lung function while the full pressure suit condition benefits by the addition of PPB. The use of pulmonary function testing as a means of determining the effect G-suit inflation has on lung volumes may prove to be ve useful in designing and evaluating the next generation of anti-G protection ensembles.
Bidirectional Certified Programming

Certiﬁed programming is one of the desirable approaches to developing dependable software, where expected properties of programs are formally proved by proof assistants such as Coq. One way for certiﬁed programming with Coq is to deﬁne a function, give proofs for its properties in Coq, and then extract a program in OCaml. Another way for certiﬁed programming with Coq is to import the deﬁnition from OCaml and give proofs for its properties in Coq. Since translations in both methods are unidirectional, we can modify only either of Coq and OCaml. That makes it hard to develop large certiﬁed programs. To solve this problem, we propose a new framework for certiﬁed programming through bidirectional transformation between Coq functions and OCaml programs. In our system, one can develop certiﬁed programs by modifying both Coq functions and OCaml programs alter-natingly. All updates of the OCaml program are reﬂected to the Coq function, and vice versa, while reusing as many parts of the original one as possible.
Novel tumor-targeting, self-assembling peptide nanofiber as a carrier for effective curcumin delivery

The poor aqueous solubility and low bioavailability of curcumin restrict its clinical application for cancer treatment. In this study, a novel tumor-targeting nanofiber carrier was developed to improve the solubility and tumor-targeting ability of curcumin using a self-assembled Nap-GFFYG-RGD peptide. The morphologies of the peptide nanofiber and the curcumin-encapsulated nanofiber were visualized by transmission electron microscopy. The tumor-targeting activity of the curcumin-encapsulated Nap-GFFYG-RGD peptide nanofiber (f-RGD-Cur) was studied in vitro and in vivo, using Nap-GFFYG-RGE peptide nanofiber (f-RGE-Cur) as the control. Curcumin was encapsulated into the peptide nanofiber, which had a diameter of approximately 10–20 nm. Curcumin showed sustained-release behavior from the nanofibers in vitro. f-RGD-Cur showed much higher cellular uptake in αvβ3 integrin-positive HepG2 liver carcinoma cells than did non-targeted f-RGE-Cur, thereby leading to significantly higher cytotoxicity. Ex vivo studies further demonstrated that curcumin could accumulate markedly in mouse tumors after administration of f-RGD-Cur via the tail vein. These results indicate that Nap-GFFYG-RGD peptide self-assembled nanofibers are a promising hydrophobic drug delivery system for targeted treatment of cancer.
Trait coordination, mechanical behaviour and growth form plasticity of Amborella trichopoda under variation in canopy openness

Finding that Amborella trichopoda is sister to the rest of the angiosperms has raised the question of whether it shares certain key functional trait characteristics and plastic responses apparently widespread within the angiosperms at large. With this in mind, Trueba et al. tested the hypothesis that local canopy openness induces plastic responses in Amborella. The authors provide evidence of intraspecific coordination between leaf and stem economic spectra in this key species. Moreover, by presenting the first architectural and biomechanical characterization of Amborella, their study offers new insights for the understanding of the early sequences of angiosperm form evolution.
The neurotrophin receptor p75NTR in Schwann cells is implicated in remyelination and motor recovery after peripheral nerve injury

The function of the p75NTR neurotrophin receptor (p75NTR) in nervous system regeneration is still controversial. Part of that controversy may be due to the fact that p75NTR is expressed by both neuronal and glial cell types and may have very distinct and even contradictory roles in each population. In this study, to elucidate the in vivo function of p75NTR in Schwann cells during remyelination after peripheral nerve injury, we established a new animal model for p75NTR‐deficient Schwann cell transplantation in nude mice. We performed quantitative assessments of the functional, histological, and electrophysiological recovery after sciatic nerve injury, and compared them with those of the p75NTR(+/+) Schwann cell transplanted animals. At 7–10 weeks after injury, the motor recovery in the p75NTR(−/−) Schwann cell transplanted animals was significantly impaired compared with that in the p75NTR(+/+) Schwann cell transplanted animals. The lower number of the retrogradely labeled motoneurons and the hypomyelination in the p75NTR(−/−) Schwann cell transplanted animals were evident at 6 and 10 weeks after injury. At 10 weeks after injury, the radial growth in the axon caliber was also impaired in the p75NTR(−/−) Schwann cell transplanted animals. Measurement of the amount of myelin proteins and the nerve conduction velocity at 10 weeks after injury reflected these results. In summary, the p75NTR expression in Schwann cells is important for remyelination process, and the motor recovery after injury is impaired due to impaired axonal growth, remyelination, and radial growth in the axon calibers. © 2007 Wiley‐Liss, Inc.
NUMERICAL MODELING OF THE 1998 PAPUA NEW GUINEA TSUNAMI USING THE COMCOT

The Papua New Guinea tsunami of 1998 is a unique phenomenon because the source of the tsunami propagation has been speculated. There was a 7.1-magnitude earthquake on July 17, 1998, at 18:49 WIT before the tsunami hit the Aitape area. However, previous studies have shown that the leading cause of the tsunami was not the earthquake but a submarine landslide. One of the steps to simulating the event is to do tsunami modeling. A tsunami propagation simulation will be conducted using Cornell Multi-grid Coupled Tsunami (COMCOT). This simulation was carried out with three scenarios to see which had the most significant effect on the tsunami event. The first scenario uses a tsunami source from a 7.1 magnitude earthquake, the following scenario is carried out using avalanche parameters, and the last scenario is a scenario with a combined source of earthquake and avalanche. The results of this study indicate that underwater landslides are the source of a tsunami similar to the original event.
Chimeric DNA-RNA hammerhead ribozyme to proliferating cell nuclear antigen reduces stent-induced stenosis in a porcine coronary model.

BACKGROUND Stent-induced coronary restenosis is a major clinical and public health problem. Proliferating cell nuclear antigen (PCNA) is an important regulator of cell division, and blocking of its expression after angioplasty may limit intimal proliferation. METHODS AND RESULTS We cloned the porcine PCNA gene and constructed a chimeric hammerhead ribozyme to a segment of the gene with human homology. In vitro studies with both cultured porcine and human vascular smooth muscle cells demonstrated uptake of ribozyme within the nucleus and significant inhibition of cellular proliferation. The ribozyme was then delivered locally into pig coronaries in a stent model. At 30 days, histomorphometric analysis showed neointimal thickness of 0.51+/-0.20 mm in the ribozyme group versus 0.71+/-0.27 and 0.66+/-0.25 mm in stent controls and scrambled ribozyme control, respectively (P=0.002, P=0.03). Quantitative angiographic analysis showed late loss of 1.4+/-0.5 mm for ribozyme versus 1.9+/-0.4 and 2.0+/-0.4 mm for the controls (P=0.05 and P=0. 02). CONCLUSIONS Chimeric hammerhead ribozyme to PCNA inhibits smooth muscle cell proliferation in vitro and reduces both histomorphometric and angiographic restenosis in the porcine coronary stent model when delivered locally.