bluuebunny/crossref_metadata_2025_split huggingface dataset:
Perfect Phylogenies via Branchings in Acyclic Digraphs and a Generalization of Dilworth’s Theorem
Authors: Hujdurović Ademir , Husić Edin , Milanić Martin , Rizzi Romeo , Tomescu Alexandru I. 
Published: April 2018

Motivated by applications in cancer genomics and following the work of Hajirasouliha and Raphael (WABI 2014), Hujdurović et al. (IEEE TCBB, 2018) introduced the minimum conflict-free row split (MCRS) problem: split each row of a given binary matrix into a bitwise OR of a set of rows so that the resulting matrix corresponds to a perfect phylogeny and has the minimum possible number of rows among all matrices with this property. Hajirasouliha and Raphael also proposed the study of a similar problem, in which the task is to minimize the number of distinct rows of the resulting matrix. Hujdurović et al. proved that both problems are NP-hard, gave a related characterization of transitively orientable graphs, and proposed a polynomial-time heuristic algorithm for the MCRS problem based on coloring cocomparability graphs.
We give new, more transparent formulations of the two problems, showing that the problems are equivalent to two optimization problems on branchings in a derived directed acyclic graph. Building on these formulations, we obtain new results on the two problems, including (1) a strengthening of the heuristic by Hujdurović et al. via a new min-max result in digraphs generalizing Dilworth’s theorem, which may be of independent interest; (2) APX-hardness results for both problems; (3) approximation algorithms; and (4) exponential-time algorithms solving the two problems to optimality faster than the naïve brute-force approach. Our work relates to several well-studied notions in combinatorial optimization: chain partitions in partially ordered sets, laminar hypergraphs, and (classical and weighted) colorings of graphs.
Data Usage Control for Distributed Systems
Authors: Kelbert Florian , Pretschner Alexander 
Published: April 2018

Data usage control enables data owners to enforce policies over how their data may be used after they have been released and accessed. We address distributed aspects of this problem, which arise if the protected data reside within multiple systems. We contribute by formalizing, implementing, and evaluating a fully decentralized system that (i) generically and transparently tracks protected data across systems, (ii) propagates data usage policies along, and (iii) efficiently and preventively enforces policies in a decentralized manner. The evaluation shows that (i) dataflow tracking and policy propagation achieve a throughput of 21--54% of native execution and (ii) decentralized policy enforcement outperforms a centralized approach in many situations.
Motif Counting Beyond Five Nodes
Authors: Bressan Marco , Chierichetti Flavio , Kumar Ravi , Leucci Stefano , Panconesi Alessandro 
Published: April 2018

Counting graphlets is a well-studied problem in graph mining and social network analysis. Recently, several papers explored very simple and natural algorithms based on Monte Carlo sampling of Markov Chains (MC), and reported encouraging results. We show, perhaps surprisingly, that such algorithms are outperformed by color coding (CC) [2], a sophisticated algorithmic technique that we extend to the case of graphlet sampling and for which we prove strong statistical guarantees. Our computational experiments on graphs with millions of nodes show CC to be more accurate than MC; furthermore, we formally show that the mixing time of the MC approach is too high in general, even when the input graph has high conductance. All this comes at a price however. While MC is very efficient in terms of space, CC’s memory requirements become demanding when the size of the input graph and that of the graphlets grow. And yet, our experiments show that CC can push the limits of the state-of-the-art, both in terms of the size of the input graph and of that of the graphlets.
Rho Kinase Inhibition by AT13148 Blocks Pancreatic Ductal Adenocarcinoma Invasion and Tumor Growth
Authors: Rath Nicola , Munro June , Cutiongco Marie Francene , Jagiełło Alicja , Gadegaard Nikolaj , McGarry Lynn , Unbekandt Mathieu , Michalopoulou Evdokia , Kamphorst Jurre J. , Sumpton David , Mackay Gillian , Vennin Claire , Pajic Marina , Timpson Paul , Olson Michael F. 
Published: April 2018

Abstract
The high mortality of pancreatic cancer demands that new therapeutic avenues be developed. The orally available small-molecule inhibitor AT13148 potently inhibits ROCK1 and ROCK2 kinases that regulate the actomyosin cytoskeleton. We previously reported that ROCK kinase expression increases with human and mouse pancreatic cancer progression and that conditional ROCK activation accelerates mortality in a genetically modified LSL-KrasG12D; LSL-p53R172H; Pdx1-Cre; (KPC) mouse pancreatic cancer model. In this study, we show that treatment of KPC mouse and human TKCC5 patient-derived pancreatic tumor cells with AT13148, as well as the ROCK-selective inhibitors Y27632 and H1152, act comparably in blocking ROCK substrate phosphorylation. AT13148, Y27632, and H1152 induced morphologic changes and reduced cellular contractile force generation, motility on pliable discontinuous substrates, and three-dimensional collagen matrix invasion. AT13148 treatment reduced subcutaneous tumor growth and blocked invasion of healthy pancreatic tissue by KPC tumor cells in vivo without affecting proliferation, suggesting a role for local tissue invasion as a contributor to primary tumor growth. These results suggest that AT13148 has antitumor properties that may be beneficial in combination therapies or in the adjuvant setting to reduce pancreatic cancer cell invasion and slow primary tumor growth. AT13148 might also have the additional benefit of enabling tumor resection by maintaining separation between tumor and healthy tissue boundaries.
Significance: Preclinical evaluation of a small-molecule ROCK inhibitor reveals significant effects on PDAC invasion and tumor growth, further validating ROCK kinases as viable therapeutic targets in pancreatic cancer. Cancer Res; 78(12); 3321–36. ©2018 AACR.
PPARγ Contributes to Immunity Induced by Cancer Cell Vaccines That Secrete GM-CSF
Authors: Goyal Girija , Wong Karrie , Nirschl Christopher J. , Souders Nicholas , Neuberg Donna , Anandasabapathy Niroshana , Dranoff Glenn 
Published: April 2018

Abstract
Peroxisome proliferator activated receptor-γ (PPARγ) is a lipid-activated nuclear receptor that promotes immune tolerance through effects on macrophages, dendritic cells (DCs), and regulatory T cells (Tregs). Granulocyte–macrophage colony stimulating factor (GM-CSF) induces PPARγ expression in multiple myeloid cell types. GM-CSF contributes to both immune tolerance and protection, but the role of PPARγ in these pathways is poorly understood. Here, we reveal an unexpected stimulatory role for PPARγ in the generation of antitumor immunity with irradiated, GM-CSF–secreting tumor-cell vaccines (GVAX). Mice harboring a deletion of pparg in lysozyme M (LysM)-expressing myeloid cells (KO) showed a decreased ratio of CD8+ T effectors to Tregs and impaired tumor rejection with GVAX. Diminished tumor protection was associated with altered DC responses and increased production of the Treg attracting chemokines CCL17 and CLL22. Correspondingly, the systemic administration of PPARγ agonists to vaccinated mice elevated the CD8+ T effector to Treg ratio through effects on myeloid cells and intensified the antitumor activity of GVAX combined with cytotoxic T lymphocyte–associated antigen-4 antibody blockade. PPARγ agonists similarly attenuated Treg induction and decreased CCL17 and CCL22 levels in cultures of human peripheral blood mononuclear cells with GM-CSF–secreting tumor cells. Together, these results highlight a key role for myeloid cell PPARγ in GM-CSF–stimulated antitumor immunity and suggest that PPARγ agonists might be useful in cancer immunotherapy. Cancer Immunol Res; 6(6); 723–32. ©2018 AACR.
Changes in Ocean Heat Content Caused by Wave-Induced Mixing in a High-Resolution Ocean Model
Authors: Stoney Lachlan , Walsh Kevin J. E. , Thomas Steven , Spence Paul , Babanin Alexander V. 
Published: April 2018

Abstract A parameterization of turbulent mixing from unbroken surface waves is included in a 16-yr simulation within a high-resolution ocean circulation model (MOM5). This “surface wave mixing” (SWM) derives from the wave orbital motion and is parameterized as an additional term in a k-epsilon model. We show that SWM leads to significant changes in sea surface temperatures but smaller changes in ocean heat content, and show the extent to which these changes can reduce pre-existing model biases with respect to observed data. Specifically, SWM leads to a widespread improvement in sea surface temperature in both hemispheres in summer and winter, while for ocean heat content the improvements are less clear. In addition, we show that introducing SWM can lead to an accumulation of wave-induced ocean heat content between years. While it has been well established that secular positive trends exist in global wave heights, we find that such trends are relatively unimportant in driving the accumulation of wave-induced ocean heat content. Rather, in response to the new source of mixing, the simulated ocean climate evolves toward a new equilibrium with greater total ocean heat content.
Effects of Vitamin B6 (Pyridoxine) and a B Complex Preparation on Dreaming and Sleep
Authors: Adventure-Heart Denholm J. , Madden Natasha A. , Delfabbro Paul 
Published: April 2018

Anecdotal evidence indicates that supplementation with vitamin B6 (pyridoxine) before bed can enhance dream vividness and recall. In a single pilot study, Ebben, Lequerica, and Spielman (2002) found that vitamin B6 had a dose-dependent effect of increasing scores on a composite measure of dream vividness, bizarreness, emotionality, and color. The present research replicated this study using a larger and more diverse sample of 100 participants from across Australia. We conducted a randomized, double-blind, placebo-controlled investigation of the effects on dreaming and sleep of ingesting 240 mg vitamin B6 (pyridoxine hydrochloride) before bed for five consecutive days. We also included an exploratory condition involving a B complex preparation containing a range of B vitamins. We found that vitamin B6 significantly increased the amount of dream content participants recalled but did not significantly affect dream vividness, bizarreness, or color, nor did it significantly affect other sleep-related variables. In contrast, participants in the B complex group showed significantly lower self-rated sleep quality and significantly higher tiredness on waking. We discuss the potential for using vitamin B6 in research on lucid dreaming. Editor's Note According to the U.S. National Library of Medicine, National Institute of Health (as promulgated by PubMed), very high doses of vitamin B6 of 1000 mg/day have been associated with neuropathy, and there have been occasional reports of toxicity at 100-300 mg/day. B6 dosages obtained naturally through foods are needed and beneficial, and this study's use of a pyridoxine hydrochloride dose of 240 mg translates to a typical B6 dose of less than 200 mg/ day and was limited to five days. Use of a B6 supplement at any higher level or on a more prolonged basis is not recommended outside of an approved research study or without close physician oversight.
The influence of natural functional clothing on some biophysical parameters of the skin
Authors: Zimniewska Malgorzata , Pawlaczyk Mariola , Krucinska Izabella , Frydrych Iwona , Mikolajczak Przemysław , Schmidt-Przewozna Katarzyna , Komisarczyk Agnieszka , Herczynska Lucyna , Romanowska Barbara 
Published: April 2018

The objectives of the study were to develop functional natural fiber clothing with microcapsules containing active herbal extracts with properties enhancing the treatment of dermatoses and to confirm the efficiency of the clothing's activity by testing its effect on the biophysical parameters of human skin. As a result of the work, clothing enriched with green tea and Viola tricolor extracts enclosed in ethyl cellulose microcapsules was produced. The microcapsules were applied on the inner surface of linen knitted fabric, which ensured direct contact of the active substances with the patients' affected skin. The efficiency of the clothing was tested according to our own methodology, which included wearing tests, microbiological tests of the skin and tests of skin moisture, transepidermal water loss and itching intensity. Also, the effect of the active substances present on the fabrics on the in vitro culture of human keratinocytes was evaluated. The test results confirmed that linen clothing enriched with medicinal plant extracts enclosed in microcapsules had an effect on the reduction of itching intensity, an increase in skin moisture, reduction of transepidermal water loss and a reduction of pathogenic bacterial colonies residing on the patients' skin. They confirmed that the new method of administering herbal substances to the skin of dermatological patients via the wearing of functional clothing is effective and leads to symptom relief. The studies allowed for the filing of a patent submission, number P 411869, titled “The clothing acting as a dressing supplement in the therapy of dermatological diseases.”
Effects of indoor water sounds on intrusive noise perception and speech recognition in rooms
Authors: Yang Wonyoung , Moon Hyeun Jun 
Published: April 2018

While water sounds have been used for soundscape improvement, little is known about their applicability in indoor environments. In order to investigate the effects of indoor water sounds on noise perception, a simple indoor water fountain system was used to produce water sounds over three different types of indoor intrusive noise (traffic noise, higher frequency dominated noise of a chair scraping the floor above, lower frequency dominated impact noise of a man running on the floor above) and speech in a test laboratory. Intrusive noise perception (annoyance and pleasantness) and speech recognition (KS-MWL-A) were assessed with three water sound levels (40, 50, 60 dBA) at two exposure times (immediate and 50 min) of water sounds by 54 participants. Short-term exposure to indoor water sounds improved the pleasantness of intrusive noise without increasing annoyance except lower frequency dominated impact noise. The increase in exposure time to indoor water sounds did not affect intrusive noise perception and speech recognition. The water to noise ratio significantly affected annoyance and pleasantness of traffic noise only; however, the level of water sounds did not significantly affect intrusive noise perception. Indoor water sounds can be used to improve intrusive noise perception except lower frequency dominated floor impact noise with no adverse effects on speech recognition dependent upon the speech to water sound ratio. Practical application: This simple indoor water fountain can be directly applied to small offices or rooms to improve intrusive noise perception. When the simple fountain produces water sounds in a room, pleasantness of traffic noise throughout window openings or higher frequency dominated noise such as chair scraping noise can be improved without increment of annoyance and decrement of speech recognition. Short-term exposure to indoor water sounds is effective to increase pleasantness of the intrusive noises.
Outcomes of emergency thoracotomy for trauma in a general hospital in Singapore
Authors: Yoong Isabelle Rui Wen , Heng Gregory , Mathur Sachin , Lim Woan Wui , Goo Tiong Thye 
Published: April 2018

Background An emergency thoracotomy can be performed either immediately at the site of trauma or in the emergency department or operating room for resuscitation of patients in extremis or life-saving treatment for patients with thoracic injury. It remains a procedure associated with high mortality rates, and there is a paucity of data from Asia. This study analyzed our six-year experience of emergency trauma thoracotomy in an acute general hospital in Singapore. Methods This retrospective analysis was based on experience in a single institution with all emergency trauma thoracotomies performed by general surgeons. All patients who underwent an emergency trauma thoracotomy in Khoo Teck Puat Hospital between January 2011 and December 2016 were studied. Data collected included patient demographics, mechanism of injury, Injury Severity Scores, surgical approach, and postoperative outcomes. Results Twenty-three patients underwent an emergency thoracotomy, 8 in the emergency department and 15 in the operating room. The mechanism of injury was blunt in 20 (87%) patients and penetrating in 3 (13%), with road traffic accidents the most common cause (70%). Six (40%) patients who underwent an emergency thoracotomy in the operating room survived beyond 24 h, and 4 (27%) survivors were eventually discharged from the hospital with no neurological deficit. No patient who underwent a thoracotomy in the emergency department survived beyond 24 h. Conclusions Emergency thoracotomy is associated with high mortality rates, especially when required in the emergency department or for blunt trauma. Nevertheless, it is a potentially life-saving procedure that offers a chance of survival in selected patients.
Myocardial protection following del Nido cardioplegia in pediatric cardiac surgery
Authors: Panigrahi Debasish , Roychowdhury Saibal , Guhabiswas Rahul , Rupert Emmanuel , Das Mrinalendu , Narayan Pradeep 
Published: April 2018

Background This study was designed to compare myocardial protection with del Nido cardioplegia and conventional blood cardioplegia in children undergoing cardiac surgery in Risk Adjustment for Congenital Heart Surgery categories 1 and 2. Methods Sixty patients were randomized into 2 groups receiving del Nido cardioplegia solution or conventional blood cardioplegia. Myocardial injury was assessed using biochemical markers (troponin I and creatine kinase-MB). Vasoactive-inotropic scores were calculated to compare inotropic requirements. Results Demographic characteristics, cardiopulmonary bypass time, and aortic crossclamp time were comparable in the 2 groups. Time-related changes in troponin I and creatine kinase-MB were similar in both groups. Statistically significant differences were seen in total cardioplegia volume requirement ( p < 0.0001), number of cardioplegia doses given ( p < 0.0001), packed red cell volume usage during cardiopulmonary bypass ( p < 0.02), and time taken to restore spontaneous regular rhythm ( p < 0.0001). Vasoactive-inotropic scores on transfer to the intensive care unit ( p < 0.040) and at 24 h ( p < 0.030) were significantly lower in the del Nido group. Duration of mechanical ventilation, intensive care unit stay, and hospital stay were comparable in the 2 groups. Conclusions Our results show that del Nido cardioplegia solution is as safe as conventional blood cardioplegia. Moreover, it provides the benefits of reduced dose requirement, lower consumption of allogenic blood on cardiopulmonary bypass, quicker resumption of spontaneous regular cardiac rhythm, and less inotropic support requirement on transfer to the intensive care unit and at 24 h, compared to conventional blood cardioplegia.
Comparative assessment and suitability of iron and the nutritional composition of fortified foods for young children
Authors: AbuKhader Majed M 
Published: April 2018

Aim: To assess the suitability of iron content and the nutritional benefits of selected fortified food products marketed for 4–8 year old children in Oman. Methods: Forty-five fortified foods, which are available in Omani markets, were classified into four groups based on food type and composition: ready-to-eat (RTE) breakfast cereals (two groups), malted milk drinks and milk powder formulas. The nutrition panel displayed on the products’ outer package was used as a source of content values for iron and other nutrients. Results: Among the selected products, malted milk drinks contain a significant ( p < 0.001) amount of iron that is 6.2±3.1 mg per 30 g serving (recommended daily intake for children 4–8 years old is 10 mg). The way selected products are served, with milk or water, could have a significant impact on the iron absorption and bioavailability, which is influenced by the presence of calcium and vitamin C. The values recorded from malted milk drinks and milk powder formulas were shown to have vitamin C to iron ratios of 3:1 and 8:1, respectively. Such ratios are reportedly effective in reversing the negative effect of calcium on iron absorption. Iron-fortified foods contain low to moderate amount of iron per serving and are considered more nutritious when compared to iron supplements. Conclusion: Iron-fortified foods can be conditionally useful to prevent or restore iron deficiency but not be relied on as an only source of iron. Hence these products must be consumed as a part of a healthy diet plan.
The ability of ADC measurements in the assessment of patients with stage I endometrial carcinoma based on three risk categories
Authors: Liu Jia , Yuan Feng , Wang Shijia , Chen Xiaojun , Ma Fenghua , Zhang Guofu , Tian Xiaomei 
Published: April 2018

Background Better selection of patients with intermediate and high-risk stage I endometrial carcinoma (EC) for lymphadenectomy has an important effect on the prognosis. Purpose To investigate the role of apparent diffusion coefficient (ADC) measurements in the assessment of stage I EC patients based on three risk categories. Material and Methods We retrospectively studied 80 patients with EC and 28 cervical cancer patients with normal endometrium. 1.5-T conventional magnetic resonance imaging (MRI) and diffusion-weighted imaging (DWI) (b = 0, 1000 s/mm2) were performed, and ADC values were calculated. Sixty-eight stage I EC patients were divided into three groups: low-risk EC (group 1); intermediate-risk EC (group 2); and high-risk EC (group 3). The remaining 12 EC patients were in stages II and III. Intraclass coefficient, Mann–Whitney U test, Kruskal–Wallis test, and receiver operating characteristics were used for statistical analysis. Results The mean ADC values ( × 10–3 mm2 /s) were 0.851 ± 0.131, 0.734 ± 0.108, and 0.710 ± 0.108 for groups 1, 2 and 3, respectively. Significant statistical differences were achieved for the three groups ( P = 0.0005). The mean ADC values of group 1 were significantly lower than those in group 2 + 3 (0.725 ± 0.106; P = 0.0001). For the prediction of groups 2 + 3, the area under the curve of 0.786 and the cut-off value of ≤ 0.742 were identified, with a sensitivity, specificity, and accuracy of 66.67%, 84.09%, and 73.53%, respectively. Conclusion ADC measurements may have the potential to select intermediate-risk and high-risk stage I EC patients for lymphadenectomy.