Miracle-dz/UniFAR-FTUs huggingface dataset:
The Structure of Apolipoprotein A-II in Discoidal High Density Lipoproteins*

It is well accepted that high levels of high density lipoproteins (HDL) reduce the risk of atherosclerosis in humans. Apolipoprotein A-I (apoA-I) and apoA-II are the first and second most common protein constituents of HDL. Unlike apoA-I, detailed structural models for apoA-II in HDL are not available. Here, we present a structural model of apoA-II in reconstituted HDL (rHDL) based on two well established experimental approaches: chemical cross-linking/mass spectrometry (MS) and internal reflection infrared spectroscopy. Homogeneous apoA-II rHDL were reacted with a cross-linking agent to link proximal lysine residues. Upon tryptic digestion, cross-linked peptides were identified by electrospray mass spectrometry. 14 cross-links were identified and confirmed by tandem mass spectrometry (MS/MS). Infrared spectroscopy indicated a beltlike molecular arrangement for apoA-II in which the protein helices wrap around the lipid bilayer rHDL disc. The cross-links were then evaluated on three potential belt arrangements. The data clearly refute a parallel model but support two antiparallel models, especially a “double hairpin” form. These models form the basis for understanding apoA-II structure in more complex HDL particles.
Identifying forensically uninteresting files in a large corpus

For digital forensics, eliminating the uninteresting is often more critical than finding the interesting since there is so much more of it. Published software-file hash values like those of the National Software Reference Library (NSRL) have limited scope. We discuss methods based on analysis of file context using the metadata of a large corpus. Tests were done with an international corpus of 262.7 million files obtained from 4018 drives. For malware investigations, we identify clues to malware in context, and show that using a Bayesian ranking formula on metadata can increase recall by 5.1 while increasing precision by 1.7 times over inspecting executables alone. For more general investigations, we show that using together two of nine criteria for uninteresting files, with exceptions for some special interesting files, can exclude 77.4% of our corpus instead of the 23.8% that were excluded by NSRL. For a test set of 19,784 randomly selected files from our corpus that were manually inspected, false positives after file exclusion (interesting files identified as uninteresting) were 0.18% and false negatives (uninteresting files identified as interesting) were 29.31% using our methods. The generality of the methods was confirmed by separately testing two halves of our corpus. Few of our excluded files were matched in two commercial hash sets. This work provides both new uninteresting hash values and programs for finding more.
Perish or Publish in China: Pressures on Young Chinese Scholars to Publish in Internationally Indexed Journals

To boost their research productivities, Chinese universities are putting great pressure on their research-active staff to publish in internationally indexed journals. However, the emerging publish-or-perish culture in China has seen little empirical investigation thus far. In the research reported in this article, semi-structured interviews were conducted with seven young researchers in science and engineering disciplines at a research-centered university in central China. The study showed that these young scholars faced great pressure to publish papers in internationally indexed journals. Consequently, the participants were reluctant to spend time on other academic activities, including teaching training. They also reported considerable work time devoted to writing, which resulted in fatigue and negatively affected family relations. The participants admitted that they had to rush to publish, and therefore were less likely to produce papers of better quality or those with novel discoveries. The research contributes to our reflection upon Chinese universities’ increasing use of the number of international publications as a major assessment and incentive measurement of their faculties’ academic performance.
Static and dynamic lengths of neutrophil microvilli.

Containing most of the L-selectin and P-selectin glycoprotein ligand-1 (PSGL-1) on their tips, microvilli are believed to promote the initial arrest of neutrophils on endothelium. At the rolling stage following arrest, the lifetimes of the involved molecular bonds depend on the pulling force imposed by the shear stress of blood flow. With two different methods, electron microscopy and micropipette manipulation, we have obtained two comparable neutrophil microvillus lengths, both approximately 0.3 microm in average. We have found also that, under a pulling force, a microvillus can be extended (microvillus extension) or a long thin membrane cylinder (a tether) can be formed from it (tether formation). If the force is </=34 pN (+/- 3 pN), the length of the microvillus will be extended; if the force is >61 pN (+/- 5 pN), a tether will be formed from the microvillus at a constant velocity, which depends linearly on the force. When the force is between 34 pN and 61 pN (transition zone), the degree of association between membrane and cytoskeleton in individual microvilli will dictate whether microvillus extension or tether formation occurs. When a microvillus is extended, it acts like a spring with a spring constant of approximately 43 pN/microm. In contrast to a rigid or nonextendible microvillus, both microvillus extension and tether formation can decrease the pulling force imposed on the adhesive bonds, and thus prolonging the persistence of the bonds at high physiological shear stresses.
Assessment of the catabolic effects of interleukin-1beta on proteoglycan metabolism in equine cartilage cocultured with synoviocytes.

OBJECTIVE To evaluate the effects of interleukin (IL)-1beta on proteoglycan metabolism in equine cartilage explants when cultured in the presence of synoviocytes. SAMPLE POPULATION Samples of cartilage and synovium collected from the femoropatellar joints of three 2- to 3-year-old horses. PROCEDURES 3 experimental groups were established: cartilage explants only, synoviocytes only, and cartilage explants-synoviocytes in coculture. In each group, samples were cultured with or without IL-1beta (10 ng/mL) for 96 hours. Glycosaminoglycan (GAG) content of cartilage and medium samples was measured by use of a spectrophotometric assay; RNA was isolated from synoviocytes and cartilage and analyzed for expression of matrix metalloproteinases (MMP)-3 and -13 (cartilage and synoviocytes), aggrecan (cartilage), collagen type IIB (cartilage), and 18S as a control (cartilage and synoviocytes) by use of quantitative PCR assays. Cartilage matrix metachromasia was assessed histochemically. RESULTS IL-1beta-induced GAG loss from cartilage was significantly less in cocultures than in cartilage-only cultures. Cartilage aggrecan gene expression was also significantly less downregulated and synoviocyte MMP-3 expression was less upregulated by IL-1beta in cocultures, compared with cartilage- and synoviocyte only cultures. Histochemical findings supported the molecular and biochemical results and revealed maintenance of matrix metachromasia in cocultured cartilage treated with IL-1beta. CONCLUSIONS AND CLINICAL RELEVANCE Results suggest that synoviocytes secrete 1 or more mediators that preferentially protect matrix GAG metabolism from the degradative effects of IL-1beta. Further studies involving proteomic and microarray approaches in similar coculture systems may elucidate novel therapeutic targets for the treatment of osteoarthritis.
[18F]fluoroestradiol radiation dosimetry in human PET studies.

UNLABELLED [18F]16alpha-fluoroestradiol (FES) is a PET imaging agent useful for the study of estrogen receptors in breast cancer. We estimated the radiation dosimetry for this tracer using data obtained in patient studies. METHODS Time-dependent tissue concentrations of radioactivity were determined from blood samples and PET images in 49 patients (52 studies) after intravenous injection of FES. Radiation absorbed doses were calculated using the procedures of the MIRD committee, taking into account the variation in dose based on the distribution of activities observed in the individual patients. Effective dose equivalent was calculated using International Commission on Radiological Protection Publication 60 weights for the standard woman. RESULTS The effective dose equivalent was 0.022 mSv/MBq (80 mrem/mCi). The organ that received the highest dose was the liver (0.13 mGy/MBq [470 mrad/mCi]), followed by the gallbladder (0.10 mGy/MBq [380 mrad/mCi]) and the urinary bladder (0.05 mGy/MBq [190 mrad/mCi]). CONCLUSION The organ doses are comparable to those associated with other commonly performed nuclear medicine tests. FES is a useful estrogen receptor-imaging agent, and the potential radiation risks associated with this study are well within accepted limits.
Your click decides your fate: Inferring Information Processing and Attrition Behavior from MOOC Video Clickstream Interactions

In this work, we explore video lecture interaction in Massive Open Online Courses (MOOCs), which is central to student learning experience on these educational platforms. As a research contribution, we operationalize video lecture clickstreams of students into cognitively plausible higher level behaviors, and construct a quantitative information processing index, which can aid instructors to better understand MOOC hurdles and reason about unsatisfactory learning outcomes. Our results illustrate how such a metric inspired by cognitive psychology can help answer critical questions regarding students' engagement, their future click interactions and participation trajectories that lead to in-video & course dropouts. Implications for research and practice are discussed
A Simple Automatic MT Evaluation Metric

This paper describes a simple evaluation metric for MT which attempts to overcome the well-known deficits of the standard BLEU metric from a slightly different angle. It employes Levenshtein's edit distance for establishing alignment between the MT output and the reference translation in order to reflect the morphological properties of highly inflected languages. It also incorporates a very simple measure expressing the differences in the word order. The paper also includes evaluation on the data from the previous SMT workshop for several language pairs.
TRUSTS: Scheduling Randomized Patrols for Fare Inspection in Transit Systems

In proof-of-payment transit systems, passengers are legally required to purchase tickets before entering but are not physically forced to do so. Instead, patrol units move about the transit system, inspecting the tickets of passengers, who face fines if caught fare evading. The deterrence of such fines depends on the unpredictability and effectiveness of the patrols. In this paper, we present TRUSTS, an application for scheduling randomized patrols for fare inspection in transit systems. TRUSTS models the problem of computing patrol strategies as a leader-follower Stackelberg game where the objective is to deter fare evasion and hence maximize revenue. This problem differs from previously studied Stackelberg settings in that the leader strategies must satisfy massive temporal and spatial constraints; moreover, unlike in these counterterrorism-motivated Stackelberg applications, a large fraction of the ridership might realistically consider fare evasion, and so the number of followers is potentially huge. A third key novelty in our work is deliberate simplification of leader strategies to make patrols easier to be executed. We present an efficient algorithm for computing such patrol strategies and present experimental results using real-world ridership data from the Los Angeles Metro Rail system. The Los Angeles County Sheriff’s department has begun trials of TRUSTS.
Crimean‐Congo hemorrhagic fever virus delays activation of the innate immune response

As a first line of defence against virus infection, mammalian cells elicit an innate immune response, characterized by secretion of type I interferons and the up‐regulation of interferon stimulated genes. Many viruses down‐regulate the innate immune responses in order to enhance their virulence. Crimean‐Congo hemorrhagic fever virus (CCHFV), a Nairovirus of the family Bunyaviridae is the causative agent of severe hemorrhagic fever in humans with high mortality. Knowledge regarding the innate immune response against CCHFV is most limited. Interestingly, in this study it is shown that replicating CCHFV delays substantially the IFN response, possibly by interfering with the activation pathway of IRF‐3. In addition, it is demonstrated that CCHFV replication is almost insensitive to subsequent treatment with interferon‐α. Once the virus is replicating, virus replication is more or less insensitive to the antiviral effects induced by the interferon. By using an interferon bioassay, it is shown that infected cells secrete interferon relatively late after infection, that is, 48 hr post‐infection. In summary, the results suggest the presence of a virulence factor encoded by CCHFV that delays the host defence in order to allow rapid viral spread in the host. J. Med. Virol. 80:1397–1404, 2008. © 2008 Wiley‐Liss, Inc.
Correlation between histopathological aspects of periodontitis and biochemical changes of oxidative stress.

PURPOSE The aim of this paper is to assess the histopathological changes and the condition of oxidative stress in the saliva of the patients with periodontal disease. MATERIALS AND METHODS We have carried out our research on two groups of patients with periodontitis (a group of 16 patients with stage I periodontitis and a group of 16 patients with stage II periodontitis), who we have compared, using samples of saliva and serum, to a group of 15 volunteers without any dental restorations. To dose MDA, we used thiobarbituric acid method and for determination of ceruloplasmin the Ravin's method. For histopathological examination, the periodontal fragments were immediately underwent for fixation in 10% neutral formalin solution and then, they were included in paraffin using the conventional histological technique. RESULTS The group of patients with stage II periodontitis presented lower values of salivary MDA compared to the group of patients with stage I periodontitis. Patients with stage I periodontitis presented a significantly increased concentration of MDA in the serum compared to the control group, but considerably lower concentrations compared to patients with stage II periodontitis. The values of serum ceruloplasmin do not present statistically important changes in patients with stage I periodontitis compared to those suffering from stage II periodontitis and to those from the group control. CONCLUSIONS MDA is not a product of blood filtration as the concentration of MDA in the bloodstream is bigger than in the saliva. Tissue changes and biochemical aspects are strongly connected. Removing dental plaque can prevent oral infections.
Integrative ecology and the dynamics of species in oak forests

Lyme disease and gypsy moth outbreaks plague many temperate oak forests. Over the past decade, we have developed models and hypotheses designed to allow us to predict irruptions of both gypsy moths and the tick vector of Lyme disease. We have documented a web of connections involving mast production by oak trees, population responses by white-footed mice, habitat selection by white-tailed deer, and population dynamics of both tick parasites and defoliating insects. In patchy landscapes typical of the northeastern U.S., dispersal by mice, deer, and attached ticks between oak and nonoak forests creates dynamics that would not be predictable by focusing on a single patch type. We would not have uncovered these interactions without adopting a research approach that comprised: (1) the inclusion of diverse taxa of animals, plants, and microbes; (2) the integration of individual, population, community, and ecosystem levels of organization; (3) the incorporation of more than one patch type in a heterogeneous landscape; and (4) a combination of long-term monitoring and manipulative field experiments.
Is the Visitor Reading or Navigating?

When a user browses a webpage, he or she generates a lot of data while moving with mouse or touchpad. The movement data hides useful information about the activity of the user. Knowing this might be useful for the perfect timing of hints online. In this paper, we propose our method for detection of browsing activity, specifically reading content and navigating. We describe our experiment in simulated news portal to acquire the dataset and we present the detection method results.
Game Analysis on the Shareholders, the Manager and the Auditor in Equity Incentive Process

Equity incentive is a two-edged sword. In this paper, a three party game model among shareholders, the manager and auditor is built to study the equity incentives negative effects. The results are: the probability of the manager and the auditors collusion to manipulate accounting information is negative connected with the shareholders punishment, and is positive connected with the monitoring cost. Shareholders should improve the technical ability and measures to punish the manager and auditor heavily when they collude to manipulate financial information; Shareholders and the regulatory agencies should give no chance to the manager and the auditor to obtain extra income from accounting information manipulation as much as possible.
Clonal spread of vancomycin resistance Enterococcus faecalis in an Iranian referral pediatrics center

Summary Vancomycin-resistant enterococci (VRE) represent as an immediate threat to public health. Since few active compounds are available for VRE infections, rapid identification of these isolates are essential. In the absence of any report on the genetic relatedness of Enterococcus faecalis especially Vancomycin-resistant E. faecalis (VREF) isolates in Iran, we undertook this study to characterize these isolates using random amplification of polymorphic DNA (RAPD–PCR) genotyping method. In this study, E. faecalis strains isolated from various samples collected from different wards of Children Medical Hospital (Tehran, Iran). These isolates were identified by standard laboratory procedures and tested for antimicrobial resistance to vancomycin and teicoplanin. The genetic similarity of the strains was investigated by amplification of the RAPD–PCR. In our study among 91 E. faecalis isolates, 15 (16%) were identified as VREF. The similarity pattern built for E. faecalis isolates by RAPD–PCR, demonstrated the presence of four distinct clusters (A, B, C, D). It is of interest to note that 100% of VREF isolates belonged to Clusters A, indicating that there may have occurred horizontal transmission of the same strain between patients. In conclusion, rapid spread of VREF from a clonal origin calls for implementation of careful isolation and infection control measures. Therefore, environmental control by routine disinfection of patient area as well as screening of high risk patients and isolation of colonized patients should be imposed in order to diminish risk of acquiring nosocomial VRE.
Lipid-based nutrient supplements do not decrease breast milk intake of Malawian infants.

BACKGROUND The potential for small-quantity lipid-based nutrient supplements (LNS) to promote growth and development after 6 mo of age is currently being investigated. Because infants self-regulate energy intake, consumption of LNS may reduce breast milk intake and potentially decrease the beneficial effects of breast milk. OBJECTIVE The objective was to test the hypothesis that the breast milk intake of 9- to 10-mo-old rural Malawian infants receiving LNS would not be lower than that of infants receiving no supplementation. DESIGN This was a substudy of the International Lipid-based Nutrient Supplements (iLiNS) DOSE trial, in which 6-mo-old infants were randomly assigned to receive 10, 20, or 40 g LNS/d containing 56, 117, or 241 kcal/d, respectively, or no LNS until 18 mo of age. A subset was randomly selected to estimate breast milk intake at 9-10 mo of age with the dose-to-mother deuterium oxide dilution method. The noninferiority margin was <10% of total energy requirements. RESULTS Baseline characteristics (n = 376) were similar across groups. The mean (± SD) daily breast milk intake of unsupplemented infants was 730 ± 226 g. The differences (95% CIs) in mean intake of infants provided with 10, 20, or 40 g LNS/d, compared with controls, were +62 (-18, +143), +30 (-40, +99), and +2 (-68, +72) g/d, respectively. Non-breast milk oral water intake did not differ by group (P = 0.39) and was inversely (r = -0.22, P < 0.01) associated with breast milk intake. CONCLUSION In this rural Malawian population, breast milk intake at 9-10 mo of age was not reduced by supplementation with complementary foods with 10-40 g LNS/d.
Mutual induction of growth factor gene expression by epidermal-dermal cell interaction

Epithelial-mesenchymal interactions control epidermal growth and differentiation, but little is known about the mechanisms of this interaction. We have examined the effects of human dermal microvascular endothelial cells (DMEC) and fibroblasts on keratinocytes in conventional (feeder layer) and organotypic cocultures (lifted collagen gels) and demonstrated the induction of paracrine growth factor gene expression. Clonal keratinocyte growth was similarly stimulated in cocultures with irradiated DMEC and fibroblasts as feeder cells. This effect is most probably caused by induction of growth factor expression in cocultured dermal cells. Keratinocytes stimulated mRNA levels for KGF and IL-6 in both mesenchymal cell types and GM-CSF in fibroblasts. The feeder effect could not be replaced by conditioned media or addition of isolated growth factors. In organotypic cocultures with keratinocytes growing on collagen gels (repopulated with dermal cells), a virtually normal epidermis was formed within 7 to 10 d. Keratinocyte proliferation was drastically stimulated by dermal cells (histone 3 mRNA expression and BrdU labeling) which continued to proliferate as well in the gel. Expression of all typical differentiation markers was provoked in the reconstituted epithelium, though with different localization as compared to normal epidermis. Keratins K1 and K10 appeared coexpressed but delayed, reflecting conditions in epidermal hyperplasia. Keratin localization and proliferation were normalized under in vivo conditions, i.e., in surface transplants on nude mice. From these data it is concluded that epidermal homeostasis is in part controlled by complex reciprocally induced paracrine acting factors in concert with cell-cell interactions and extracellular matrix influences.
Information Technology, Productivity and Asset Ownership: Evidence from Taxicab Fleets

We develop a simple model that links the adoption of a productivity-enhancing technology to increased vertical integration and a less skilled workforce. We test the model’s key prediction using novel microdata on vehicle ownership patterns from the Economic Census during a period when computerized dispatching systems were first adopted by taxicab firms. Controlling for time-invariant firm-specific effects, firms increase the proportion of taxicabs under fleet ownership by 12% when they adopt new computerized dispatching systems. An instrumental variables analysis suggests that the link between dispatching technology and vertical integration is causal. These findings suggest that increasing a firm’s productivity can lead to increased vertical integration, even in the absence of asset specificity.