Miracle-dz/UniFAR-FTUs huggingface dataset:
Peptidomic Identification of Serum Peptides Diagnosing Preeclampsia

We sought to identify serological markers capable of diagnosing preeclampsia (PE). We performed serum peptide analysis (liquid chromatography mass spectrometry) of 62 unique samples from 31 PE patients and 31 healthy pregnant controls, with two-thirds used as a training set and the other third as a testing set. Differential serum peptide profiling identified 52 significant serum peptides, and a 19-peptide panel collectively discriminating PE in training sets (n = 21 PE, n = 21 control; specificity = 85.7% and sensitivity = 100%) and testing sets (n = 10 PE, n = 10 control; specificity = 80% and sensitivity = 100%). The panel peptides were derived from 6 different protein precursors: 13 from fibrinogen alpha (FGA), 1 from alpha-1-antitrypsin (A1AT), 1 from apolipoprotein L1 (APO-L1), 1 from inter-alpha-trypsin inhibitor heavy chain H4 (ITIH4), 2 from kininogen-1 (KNG1), and 1 from thymosin beta-4 (TMSB4). We concluded that serum peptides can accurately discriminate active PE. Measurement of a 19-peptide panel could be performed quickly and in a quantitative mass spectrometric platform available in clinical laboratories. This serum peptide panel quantification could provide clinical utility in predicting PE or differential diagnosis of PE from confounding chronic hypertension.
Score for neonatal acute physiology II predicts mortality and persistent organ dysfunction in neonates with severe septicemia.

OBJECTIVE To investigate the relationship between score for neonatal acute physiology II (SNAP II) applied within 12 hours from the onset of severe sepsis, and death and persistent organ dysfunction (OD). DESIGN Prospective cohort study. SETTING Level III neonatal intensive care unit. PARTICIPANTS Neonates with severe sepsis. INTERVENTION SNAP II was applied within the first 12 hours from the onset of severe sepsis. Neonates with major malformations, severe asphyxia and prior blood products were excluded. MAJOR OUTCOME MEASURE: Death at day 14 from enrolment. RESULTS Forty neonates completed the study. Twenty-five died within 14 days. The median SNAP II was significantly higher in babies who died versus those who survived [median (IQR): 43 (36-53.5) vs 18 (16-37), P<0.001]. A SNAP II greater than 40 had 88% positive predictive value for death and persistent OD each, and 86.6% and 86% specificity for death and persistent OD, respectively. On day 14 from enrolment, more organs normalized/improved in the subjects with SNAP II of < or = 40. Perfusion related SNAP II parameters were significantly associated with death and organ dysfunction. CONCLUSIONS Severely septicemic neonates with high SNAP II scores (>40) have a higher risk of dying and persistent organ dysfunction. Individual SNAP II parameters do not contribute equally in prediction of mortality.
Early effect of intra-arterial treatment in ischemic stroke on aphasia recovery in MR CLEAN

Objective: To investigate the effect of intra-arterial treatment (IAT) on early recovery from aphasia in acute ischemic stroke. We hypothesized that the early effect of IAT on aphasia is smaller than the effect on motor deficits. Methods: We included patients with aphasia from the Multicenter Randomized Clinical Trial of Endovascular Treatment for Acute Ischemic Stroke in the Netherlands (MR CLEAN), in which 500 patients with a proximal anterior circulation stroke were randomized to usual care plus IAT (<6 hours after stroke, mainly stent retrievers) or usual care alone. We estimated the effect of IAT on the shift on the NIH Stroke Scale (NIHSS) item language and the NIHSS item motor arm at 24 hours and 1 week after stroke with multivariable ordinal logistic regression as a common odds ratio, adjusted for prognostic variables (acOR). Differences between the effect of IAT on aphasia and on motor deficits were tested in a multilevel model with a multiplicative interaction term. Results: Of the 288 patients with aphasia, 126 were assigned to IAT and 162 to usual care alone. The acOR for improvement of language score at 24 hours was 1.65 (95% confidence interval [CI] 1.05–2.60), and at 1 week 1.86 (95% CI 1.18–2.94). The acOR for improvement of motor deficit at 24 hours was 2.44 (95% CI 1.54–3.88), and at 1 week 2.32 (95% CI 1.43–3.77). The effect of IAT on language deficits was significantly different from the effect on motor deficits at 24 hours and 1 week (p = 0.005 and p = 0.011). Conclusions: IAT results in better early recovery from aphasia than usual care alone. The early effect of IAT on aphasia is smaller than the effect on motor deficits. Classification of evidence: This study provides Class II evidence that for patients with acute ischemic stroke IAT increases early recovery from aphasia and that the early effect on aphasia, as measured by the NIHSS, is smaller than the effect on motor deficits.
Exploring the Racial Divide: Blacks, Whites, and Opinion on National Policy

Black and white Americans disagree consistently and often substantially in their views on national policy. This racial divide is most pronounced on policies that intrude conspicuously on the fortunes of blacks and whites, but it is also apparent on a wide array of social welfare issues where race is less obviously in play. Our analysis takes up the question of why blacks and whites differ so markedly, distin- guishing among four alternative inter- pretations: one centers attention on underlying differences of class, an- other on political principles, a third on social identity, and the fourth on audi- ence. Our results are complicated but coherent. We discuss their implica- tions for the meaning of group inter- est, speculate on the conditions un- der which the racial divide might close (or widen) in the foreseeable future, and suggest why we should not wish racial differences in opinion to disappear.
An annual pattern of native embolism in upper branches of four tall conifer species.

PREMISE OF THE STUDY The Pacific Northwest of North America experiences relatively mild winters and dry summers. For the tall coniferous trees that grow in this region, we predicted that loss in the hydraulic conductivity of uppermost branches would be avoided because of difficulty reversing accumulated emboli in xylem that is always under negative pressure. METHODS To test this hypothesis, we measured native percent loss in hydraulic conductivity (PLC; the decrease of in situ hydraulic conductivity relative to the maximum) monthly throughout 2009 in branches at the tops (∼50 m) of four species in an old growth forest in southern Washington. KEY RESULTS Contrary to our prediction, freeze-thaw cycles resulted in considerable native PLC. Branches showed hydraulic recovery in the spring and after a moderate increase in native embolism that was observed after an unusually hot period in August. The September recovery occurred despite decreases in the leaf and stem water potentials compared to August values. CONCLUSIONS Recoveries in branches of these trees could not have occurred by raising the water potential enough to dissolve bubbles simply by transporting water from roots and must have occurred either through water absorption through needles and/or refilling under negative pressure. Excluding the August value, native embolism values correlated strongly with air temperature of the preceding 10 d. For three species, we found that branches with lower wood density had higher specific conductivity, but not greater native PLC than branches with higher wood density, which calls into question whether there is any hydraulic benefit to higher wood density in small branches in those species.
Depth: a web server to compute depth, cavity sizes, detect potential small-molecule ligand-binding cavities and predict the pKa of ionizable residues in proteins

Residue depth accurately measures burial and parameterizes local protein environment. Depth is the distance of any atom/residue to the closest bulk water. We consider the non-bulk waters to occupy cavities, whose volumes are determined using a Voronoi procedure. Our estimation of cavity sizes is statistically superior to estimates made by CASTp and VOIDOO, and on par with McVol over a data set of 40 cavities. Our calculated cavity volumes correlated best with the experimentally determined destabilization of 34 mutants from five proteins. Some of the cavities identified are capable of binding small molecule ligands. In this study, we have enhanced our depth-based predictions of binding sites by including evolutionary information. We have demonstrated that on a database (LigASite) of ∼200 proteins, we perform on par with ConCavity and better than MetaPocket 2.0. Our predictions, while less sensitive, are more specific and precise. Finally, we use depth (and other features) to predict pKas of GLU, ASP, LYS and HIS residues. Our results produce an average error of just <1 pH unit over 60 predictions. Our simple empirical method is statistically on par with two and superior to three other methods while inferior to only one. The DEPTH server (http://mspc.bii.a-star.edu.sg/depth/) is an ideal tool for rapid yet accurate structural analyses of protein structures.
University of Groningen Skeleton-Based Edge Bundling for Graph Visualization

In this paper, we present a novel approach for constructing bundled layouts of general graphs. As layout cues for bundles, we use medial axes, or skeletons, of edges which are similar in terms of position information. We combine edge clustering, distance fields, and 2D skeletonization to construct progressively bundled layouts for general graphs by iteratively attracting edges towards the centerlines of level sets of their distance fields. Apart from clustering, our entire pipeline is image-based with an efficient implementation in graphics hardware. Besides speed and implementation simplicity, our method allows explicit control of the emphasis on structure of the bundled layout, i.e. the creation of strongly branching (organic-like) or smooth bundles. We demonstrate our method on several large real-world graphs.
Secure Goods Supply Chain and Key Exchange with Virtual Proof of Reality

A new security protocol of virtual proof of reality (VP) is recently proposed by Ruhrmair et al. The VP allows one party, the prover, making a physical statement to the other party, the verifier, over a digital communication channel without using any secret keys except the message sent between these two parties. The physical statement could be a physical feature—eg. temperature—or phenomena—eg. destruction— of the hardware in the prover’s system. We present two applications— secure key exchange and secure goods supply chain—building on the VP of temperature, location, and destruction. Moreover, we experimentally demonstrate the first electrical circuit-based VP of destruction through the proposed hardware security primitive—a hybrid memristor and physical unclonable function (memristor-PUF) architecture, which takes advantage of the PUF extracted from static variations of CMOS devices inherent to the fabrication process and dynamic variations attributed to switching variabilities of nano memristors.
Murine Cytomegalovirus Infection Induces Susceptibility to EAE in Resistant BALB/c Mice

In contrast to C57BL/6 mice, BALB/c mice are relatively resistant to the induction of experimental autoimmune encephalomyelitis (EAE) after challenge with MOG35–55 peptide. Here, we provide the first evidence that infection with murine cytomegalovirus (MCMV) in adulthood abrogates this resistance. Infected BALB/c mice developed clinical and histological signs similar to those seen in susceptible C57BL/6 mice. In addition to CD4+ cells, large proportion of cells in the infiltrate of diseased BALB/c mice was CD8+, similar with findings in multiple sclerosis. CD8+ cells that responded to ex vivo restimulation with MOG35–55 were not specific for viral epitopes pp89 and m164. MCMV infection favors proinflammatory type of dendritic cells (CD86+CD40+CD11c+) in the peripheral lymph organs, M1 type of microglia in central nervous system, and increases development of Th1/Th17 encephalitogenic cells. This study indicates that MCMV may enhance autoimmune neuropathology and abrogate inherent resistance to EAE in mouse strain by enhancing proinflammatory phenotype of antigen-presenting cells, Th1/Th17, and CD8 response to MOG35–55.
"Billions and Billions Served" Heterogeneous Effects of Food Source on Child Dietary Quality

This paper estimates heterogeneous effects of food source (food away from home, at home and from school) on child dietary quality. Using a quantile estimator designed for panel data, two non-consecutive days of intake are used to identify the effiect of food source across the unconditional distribution of dietary quality. Main results suggest that food away from home has a negative impact on dietary quality for all children except those falling in the very lowest portion of the unconditional distribution. As compared to home-prepared food, school food is found to increase dietary quality for children falling in the bottom quartile of the distribution. For children with a very high underlying proneness to consume a healthful diet, food from school has a negative effect. While food consumed under the National School Lunch and Breakfast Programs may not benefit every child (especially at the mean), it does improve the diets of many children whom otherwise would have poorer dietary quality. The implication is that U.S. schools are fertile grounds to improve nutrition skill formation, especially for the most disadvantaged.
Occult Hepatitis C Virus Infection in Candidates for Liver Transplant With Cryptogenic Cirrhosis

Background Occult hepatitis C virus (HCV) infection is a new entity described by the presence of HCV-RNA in liver biopsy and/or peripheral blood mononuclear cell (PBMC) specimens, and undetectable levels or absence of HCV-RNA and in the absence or presence of anti HCV antibodies in plasma by current laboratory methods. Objectives To evaluate the detection of HCV-RNA in PBMC specimens of the liver transplant candidates with cryptogenic cirrhosis by reverse transcriptase-nested polymerase chain reaction (RT-nested PCR). Patients and Methods From November 2007 to March 2013, 45 patients from Liver Transplant Center of Imam Khomeini Hospital, Tehran, were enrolled in this cross sectional study. PBMC specimens were separated from the peripheral blood sample. After extraction of RNA from plasma and PBMC specimens, HCV-RNA status was tested by RT-nested PCR. The 5′-untranslated region (5′-UTR) genotyping of HCV-RNA amplified from PBMC specimens was performed by a standard methodology with the INNO-LiPATM HCV II kit. The PCR products of 5′-UTR were sequenced after cloning into the pJET1.2 / blunt cloning vector. Results Of 45 patients, 4 (8.9% [95% CI: 4.4-15.6]) had detectable genomic HCV-RNA in their PBMC specimens. HCV genotypes were determined in the PBMCs of these subjects showed that 2 (50.0%) subjects with occult HCV infection had HCV subtype 3a, and 2 (50.0%) had HCV subtype 1b. Conclusions This study found that 8.9 % of the Iranian candidates for liver transplant with cryptogenic cirrhosis had occult HCV infection. Therefore, designing prospective studies focusing on the diagnosis of occult HCV infection in these subjects prior to liver transplantation could be valuable.
In Situ Electrochemical SFG/DFG Study of CN− and Nitrile Adsorption at Au from 1-Butyl-1-methyl-pyrrolidinium Bis(trifluoromethylsulfonyl) Amide Ionic Liquid ([BMP][TFSA]) Containing 4-{2-[1-(2-Cyanoethyl)-1,2,3,4-tetrahydroquinolin-6-yl]diazenyl} Benzonitrile (CTDB) and K[Au(CN)2]

In this paper we report an in situ electrochemical Sum-/Difference Frequency Generation (SFG/DFG) spectroscopy investigation of the adsorption of nitrile and CN− from the ionic liquid 1-butyl-1-methyl-pyrrolidinium bis(trifluoromethylsulfonyl) amide ([BMP][TFSA]) containing 4-{2-[1-(2-cyanoethyl)-1,2,3,4-tetrahydroquinolin-6-yl]- diazenyl}benzonitrile (CTDB) at Au electrodes in the absence and in the presence of the Au-electrodeposition process from K[Au(CN)2]. The adsorption of nitrile and its coadsorption with CN− resulting either from the cathodic decomposition of the dye or from ligand release from the Au(I) cyanocomplex yield potential-dependent single or double SFG bands in the range 2,125–2,140 cm−1, exhibiting Stark tuning values of ca. 3 and 1 cm−1 V−1 in the absence and presence of electrodeposition, respectively. The low Stark tuning found during electrodeposition correlates with the cathodic inhibiting effect of CTDB, giving rise to its levelling properties. The essential insensitivity of the other DFG parameters to the electrodeposition process is due to the growth of smooth Au.
A scalable method for the generation of small test sets

This paper presents a scalable method to generate close to minimal size test pattern sets for stuck-at faults in scan based circuits. The method creates sets of potentially compatible faults based on necessary assignments. It guides the justification and propagation decisions to create patterns that will accommodate most targeted faults. The technique presented achieves close to minimal test pattern sets for ISCAS circuits. For industrial circuits it achieves much smaller test pattern sets than other methods in designs sensitive to decision order used in ATPG.
The VideoWindow System in Informal Communications

Imagine sitting in your work place lounge having coffee with some colleagues. Now imagine that you and your colleagues are still in the same room, but are separated by a large sheet of glass that does not interfere with your ability to carry on a clear, two-way conversation. Finally, imagine that you have split the room into two parts and moved one part 50 miles down the road, without impairing the quality of your interaction with your friends. That scenario illustrates the goal of the VideoWindow system project: to extend a shared space over considerable distance without impairing the quality of the interactions among users or requiring any special actions to establish a conversation. While the VideoWindow system -a very large screen, full duplex teleconferencing technology that we will describe later in this paper -cannot yet achieve this goal, we believe it can come closer to it than any other system yet invented.
Analysis of FPGA Simultaneous Switching Noise in Three Domains: Time, Frequency, and Spectrum

Simultaneous switching noise (SSN) and its behavior have become increasingly important in high-performance FPGA system design featuring hundreds of I/Os transmitting in parallel at low supply voltage standard. In this paper, we present an indepth study on SSN by analyzing its behavior in three different domains: time, frequency, and noise spectrum. Cross correlation in these three domains reveals two dominant cause mechanisms: frequency dependent PDN impedance and crosstalk from package-PCB breakout region. Each mechanism has its manifestation in time-domain SSN waveform. Furthermore, simulation confirms our postulations made on examination of experimental data and validates the methodology practical to SSN assessment in FPGA applications.
Immune Modulation in Glaucoma – Can Manipulation of Microglial Activation Help?

A large body of experimental results from clinical and experimental studies has strongly suggested an aberrant activity of the immune system in glaucoma. The roles of the innate immune responses in glaucoma are unclear and have been controversial about the concept of neuroprotection or neurodestruction. Protective immunity has been suggested occurring as a homeostatic response to injury, which can prevent disease progression. Neurodegeneration of retinal ganglion cells (RGCs) may be the consequence from a failure of proper controls for the initial immune response right after injury in some glaucoma patients. Long-term tissue stress in glaucomatous eyes appears to be important for the balance between neuroprotective and neurodestructive immunity. The onset, progression, and termination of retinal specific immune responses are predominantly regulated by the interaction among the RGCs and different glia (astrocytes, Muller cells and microglia) in the glaucomatous eyes. As immunocompetent cell in the central nervous system (CNS), microglia have diverse phenotypes and produce beneficial or destructive factors depending on the microenvironments they encounter. In response to injury, activated microglia have been shown to trigger neuronal death by producing high levels of cytotoxic factors such as nitric oxide, superoxide and tumor necrosis factor-α (TNF-α). However, increasing lines of evidence have shown that microglia can elicit protective effects by releasing trophic and anti-inflammatory factors. To transform microglia into neuroprotective or neurodestructive depends on the disease state or the type of stimulus to trigger them into “classically activated” proinflammatory (M1) or “alternatively activated” anti-inflammatory (M2) cells (Polazzi and Monti, 2010). In vitro study have shown that it is possible to manipulate the activation state of microglia so that their activation can be beneficial, i.e., protecting rather than destroying neurons (Polazzi et al., 2001; 2009). However, it is difficult to achieve this goal in vivo, especially in chronic neurodegenerative model. Our studies focus on modulating the retinal microglial cells by application of chemokine, monocytechemoattractive protein-1 (MCP-1/CCL2) into the posterior chamber to provide direct circumstance for attracting microglia to the retina. Furthermore, we also try to evaluate whether modulation of microglia in the retina can be achieved by the anti-aging Chinese medicine wolfberry. In this review, we will demonstrate how basic science research can be further developed and translated into pharmacological interventions through modulating the activation of microglia to prevent RGC loss in experimental glaucoma. This kind of approach can be one of therapeutic interventions for glaucoma patients in future.
Articulatory trajectories for large-vocabulary speech recognition

Studies have demonstrated that articulatory information can model speech variability effectively and can potentially help to improve speech recognition performance. Most of the studies involving articulatory information have focused on effectively estimating them from speech, and few studies have actually used such features for speech recognition. Speech recognition studies using articulatory information have been mostly confined to digit or medium vocabulary speech recognition, and efforts to incorporate them into large vocabulary systems have been limited. We present a neural network model to estimate articulatory trajectories from speech signals where the model was trained using synthetic speech signals generated by Haskins Laboratories' task-dynamic model of speech production. The trained model was applied to natural speech, and the estimated articulatory trajectories obtained from the models were used in conjunction with standard cepstral features to train acoustic models for large-vocabulary recognition systems. Two different large-vocabulary English datasets were used in the experiments reported here. Results indicate that employing articulatory information improves speech recognition performance not only under clean conditions but also under noisy background conditions. Perceptually motivated robust features were also explored in this study and the best performance was obtained when systems based on articulatory, standard cepstral and perceptually motivated feature were all combined.