Miracle-dz/UniFAR-FTUs huggingface dataset:
Robust Kernel Low-Rank Representation

Recently, low-rank representation (LRR) has shown promising performance in many real-world applications such as face clustering. However, LRR may not achieve satisfactory results when dealing with the data from nonlinear subspaces, since it is originally designed to handle the data from linear subspaces in the input space. Meanwhile, the kernel-based methods deal with the nonlinear data by mapping it from the original input space to a new feature space through a kernel-induced mapping. To effectively cope with the nonlinear data, we first propose the kernelized version of LRR in the clean data case. We also present a closed-form solution for the resultant optimization problem. Moreover, to handle corrupted data, we propose the robust kernel LRR (RKLRR) approach, and develop an efficient optimization algorithm to solve it based on the alternating direction method. In particular, we show that both the subproblems in our optimization algorithm can be efficiently and exactly solved, and it is guaranteed to obtain a globally optimal solution. Besides, our proposed algorithm can also solve the original LRR problem, which is a special case of our RKLRR when using the linear kernel. In addition, based on our new optimization technique, the kernelization of some variants of LRR can be similarly achieved. Comprehensive experiments on synthetic data sets and real-world data sets clearly demonstrate the efficiency of our algorithm, as well as the effectiveness of RKLRR and the kernelization of two variants of LRR.
Phrase Dependency Machine Translation with Quasi-Synchronous Tree-to-Tree Features

Recent research has shown clear improvement in translation quality by exploiting linguistic syntax for either the source or target language. However, when using syntax for both languages (“tree-to-tree” translation), there is evidence that syntactic divergence can hamper the extraction of useful rules (Ding and Palmer 2005). Smith and Eisner (2006) introduced quasi-synchronous grammar, a formalism that treats non-isomorphic structure softly using features rather than hard constraints. Although a natural fit for translation modeling, its flexibility has proved challenging for building real-world systems. In this article, we present a tree-to-tree machine translation system inspired by quasi-synchronous grammar. The core of our approach is a new model that combines phrases and dependency syntax, integrating the advantages of phrase-based and syntax-based translation. We report statistically significant improvements over a phrase-based baseline on five of seven test sets across four language pairs. We also present encouraging preliminary results on the use of unsupervised dependency parsing for syntax-based machine translation.
Sensitivity of Maize Yield Potential to Regional Climate in the Southwestern U.S.

The sensitivity of maize yields to the regional climate in the Southwestern U.S. (SWUS) has been investigated by using the Agricultural Production Systems sIMulator (APSIM) model in conjunction with meteorological forcings [daily maximum and minimum temperature (Tmax and Tmin), precipitation, and radiation] from the North American Regional Reanalysis (NARR) dataset. Sensitivity experiments showed that potential crop production responded nonlinearly to variations in Tmax, Tmin, and downwelling solar radiation at the surface. Mean annual yield potential (Yp) was changed by -3.0 and 1.79 Mg ha-1 for the +1 and -1 standard deviations (σ) of Tmax variation for entire the SWUS. The impact of Tmin changes were opposite to that of Tmax, with 2.84 and -5.11 Mg ha-1, respectively. Radiation changes only affected Yp decreases by 3.02 Mg ha-1 in the -1 σ case. Yield sensitivity varied geographically according to regional mean climate states. For warmer areas of the SWUS, including southern California and Arizona, maize productivity responded positively to a lower Tmax and higher Tmin. For cooler regions, such as northern California and high-elevation Nevada, a higher Tmax and higher Tmin were favorable for higher yields. The Tmin effect (e.g., cold surges) was larger during the planting period, and the Tmax effect (e.g., heat waves) was larger in the growing season. Downwelling solar radiation at the surface also played an important role in coastal regions and the Central Valley of California.
The soluble transcobalamin receptor (sCD320) in relation to Alzheimer’s disease and cognitive scores

Abstract The soluble transcobalamin receptor (sCD320) is present in cerebrospinal fluid and correlates with the dementia-related biomarkers phospho-tau and total-tau. Here we present data on the relation of sCD320 to Alzheimer’s disease and scores of cognitive tests. Lumbar cerebrospinal fluid samples from 42 pathologically-confirmed cases of Alzheimer’s disease and 25 non-demented controls were analyzed for sCD320 employing an in-house ELISA. The participants’ cognitive functions were tested using the Cambridge Cognition Examination (CAMCOG) and the Mini-Mental State Examination (MMSE). There was no significant difference in the median CSF sCD320 concentration between patients and controls. The median (2.5–97.5 percentiles) sCD320 for all participants (n = 67) was 15 (3–29) pmol/L. We observed a non-linear correlation between sCD320 and cognitive scores. Spearman’s correlation between sCD320 and total CAMCOG scores was 0.627 (n = 16, p = .009) for CAMCOG scores ≤27, and −0.293 (n = 39, p = .071) for CAMCOG scores ≥68. Spearman’s correlation between sCD320 and both the low (≤9) and high (≥16) total MMSE scores was 0.274, −0.363 (n = 18, 44), p = . 272, . 016, respectively. In conclusion, sCD320 cannot be employed as a biomarker for differentiating Alzheimer dementia patients from controls. Further studies are warranted to explore the non-linear correlations between sCD320 and scores of cognitive function.
Cooling Stacking Injection in NICA Booster

The multi cycling injection from the linear accelerator to the NICA booster is planned to use for storage of Au31+ ions at energy 3.1 MeV/u. The intensity of the stored ions is increased by 3-5 times at injection intensity of 5108109 ppp. The intensity of the stored beam is higher by one order of magnitude comparing with injection intensity of 108 ppp. The maximal intensity is restricted by the incoherent diffusion heating of the stack and the ion life time. The simulations of the cooling stacking injection were performed by BETACOL code. The coherent instability can be developed at a high ion intensity in presence of the electron cooling. The increment of instability essentially depends on the choice of the working point.
Rigorous Numerics in Dynamics

Motivation Nonlinear dynamics shape the world around us, from the harmonious movements of celestial bodies, via the swirling motions in fluid flows, to the complicated biochemistry in the living cell. Mathematically these beautiful phenomena are modeled by nonlinear dynamical systems, mainly in the form of ordinary differential equations (ODEs), partial differential equations (PDEs) and delay differential equations (DDEs). The presence of nonlinearities severely complicates the mathematical analysis of these dynamical systems, and the difficulties are even greater for PDEs and DDEs, which are naturally defined on infinite-dimensional function spaces. With the availability of powerful computers and sophisticated software, numerical simulations have quickly become the primary tool to study the models. However, while the pace of progress increases, one may ask: just how reliable are our computations? Even for finite-dimensional ODEs, this question naturally arises if the system under study is chaotic, as small differences in initial conditions (such as those due to rounding errors in numerical computations) yield wildly diverging outcomes. These issues have motivated the development of the field of rigorous numerics in dynamics. Rigorous numerics draws inspiration from the ideas in scientific computing, numerical analysis,
Running title : Suillus luteus inhibits proliferation of a colon cancer cell line Suillus luteus methanolic extract inhibits cell growth and proliferation of a colon cancer cell line

Cancer Drug Resistance Group, IPATIMUP – Institute of Molecular Pathology and Immunology of the University of Porto, Porto, Portugal CEQUIMED-UPCentre of Medicinal Chemistry of the University of Porto, Porto, Portugal Mountain Research Centre (CIMO), Polytechnic Institute of Bragança, Campus de Santa Apolónia, Apartado 1172, 5301-855 Bragança, Portugal Center of Chemistry, University of Minho, Campus de Gualtar 4710-057 Braga, Portugal Laboratory of Microbiology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, Portugal
Tetraneura ulmi (Hemiptera: Eriosomatinae) Induces Oxidative Stress and Alters Antioxidant Enzyme Activities in Elm Leaves

Abstract Gall formation is induced by an insect, which changes normal plant development and results in the formation of a new organ, following distinct stages of metabolic and developmental alterations. Research on mechanisms of recognition and responses to biotic stress may help to understand the interactions between galling aphids and their host plants. In this study, Tetraneura ulmi L. (Hemiptera: Eriosomatinae) galls and Ulmus pumila L. (Rosales: Ulmaceae) leaves were used as a model. Concentrations of hydrogen peroxide (H2O2) and thiobarbituric acid reactive substances, electrolyte leakage, as well as the activity of ascorbate peroxidase, guaiacol peroxidase, and catalase (CAT) were determined in galls and two parts of galled leaves (with and without visible damage). Biochemical analyses were performed at three stages of gall development: initial, fully developed, and mature galls. A slight increment in H2O2 content with a strong enhancement of ascorbate peroxidase and CAT activities were observed in galls and galled leaves in the first stage. In subsequent stages of gall development, a progressing increase in H2O2 production and cell membrane damage was associated with declining antioxidant enzyme activities, especially in gall tissues. The stages of gall development are likely to be part of cell death triggered by aphid feeding. It seems that the gall is the result of a biochemical struggle between the host plant and the gall inducer.
Single-neuron identification of chemical constituents, physiological changes, and metabolism using mass spectrometry

Significance We anticipate that our proposed single-neuron mass spectrometry technology may provide not only the possibility to study single-cell metabolism, but also the chance to investigate chemical changes in the content and metabolism of intracellular small molecules at the single-cell level during physiological processes, such as growth and development, or pathological processes, such as depression, dementia, inflammation, cancer, and other diseases. The use of single-cell assays has emerged as a cutting-edge technique during the past decade. Although single-cell mass spectrometry (MS) has recently achieved remarkable results, deep biological insights have not yet been obtained, probably because of various technical issues, including the unavoidable use of matrices, the inability to maintain cell viability, low throughput because of sample pretreatment, and the lack of recordings of cell physiological activities from the same cell. In this study, we describe a patch clamp/MS-based platform that enables the sensitive, rapid, and in situ chemical profiling of single living neurons. This approach integrates modified patch clamp technique and modified MS measurements to directly collect and detect nanoliter-scale samples from the cytoplasm of single neurons in mice brain slices. Abundant possible cytoplasmic constituents were detected in a single neuron at a relatively fast rate, and over 50 metabolites were identified in this study. The advantages of direct, rapid, and in situ sampling and analysis enabled us to measure the biological activities of the cytoplasmic constituents in a single neuron, including comparing neuron types by cytoplasmic chemical constituents; observing changes in constituent concentrations as the physiological conditions, such as age, vary; and identifying the metabolic pathways of small molecules.
Selection in the Introgressed Regions of the Chimpanzee Genome

Abstract During the demographic history of the Pan clade, there has been gene-flow between species, likely >200,000 years ago. Bonobo haplotypes in three subspecies of chimpanzee have been identified to be segregating in modern-day chimpanzee populations, suggesting that these haplotypes, with increased differentiation, may be a target of natural selection. Here, we investigate signatures of adaptive introgression within the bonobo-like haplotypes in chimpanzees using site frequency spectrum-based tests. We find evidence for subspecies-specific adaptations in introgressed regions involved with male reproduction in central chimpanzees, the immune system in eastern chimpanzees, female reproduction and the nervous system in Nigeria-Cameroon chimpanzees. Furthermore, our results indicate signatures of balancing selection in some of the putatively introgressed regions. This might be the product of long-term balancing selection resulting in a similar genomic signature as introgression, or possibly balancing selection acting on alleles reintroduced through gene flow.
Shelf recruitment of Calanus finmarchicus off the west coast of Norway: role of physical processes and timing of diapause termination

The copepod Calanus finmarchicus is an important part of the Norwegian Sea ecosys- tem because of its dominating abundance and importance as prey for fish larvae and adult plankti- vorous fish. The abundance of C. finmarchicus on the Norwegian shelf is generally low in winter, whereas in spring the shelf is replenished by individuals that overwinter at depth, either in fjords or in the deep basins of the Norwegian Sea. In the present study shelf recruitment is investigated using an individual-based model for C. finmarchicus coupled to the HYbrid Coordinate Ocean Model and a biophysical model. The model was set up on a nested grid along the west coast of Norway and used to study the shelf recruitment originating from the Norwegian Sea. We investigate the effect of wind, currents and the timing of Calanus ascent on the shelf abundance of C. finmarchicus. The most important findings are the following: (1) periods of large on-shelf transport are connected with strong westerly winds associated with passing low-pressure systems; (2) the transport of overwintering adults onto the shelf determines the total shelf abundance prior to mid-summer; (3) the early spring bloom on the shelf causes increased shelf population of C. finmarchicus in the spring and throughout the summer compared to the areas further off-shore; and (4) the entry routes taken by C. finmarchi- cus are related to bathymetry; in particular, the deep trenches around Halten Bank and the Norwe- gian trench are favoured places to enter the Norwegian shelf.
Particulate granulation and rheology : towards a unifying perspective

The mixing of powders and liquids is a process ubiquitous to many industrial, research and household applications, from the production of foodstuffs, pharmaceutical and cosmetic products to the preparation of hot drinks or cement. The final mixed state of powders and liquids can be broadly split into two distinct regimes identified respectively as having lowand high volume fraction, φ. Low-φ systems are typified by flowing suspensions whereas samples prepared with highφ, beyond some threshold value, produce solid agglomerates which are unable to flow. These two regimes are the focus of two separate scientific disciplines; suspension rheology and granulation. Within the field of suspension rheology there has been recent advances in the understanding of a phenomena known as shear thickening, which describes the increase in a suspension’s viscosity with increasing applied stress. In this thesis we aim to unify the phenomena of shear thickening and granulation within this new theoretical framework. We study shear thickening and granulation using a well characterised model system developed for this purpose, comprising polydisperse glass particles with a mean diameter of ' 7 μm and a glycerol-water mixture (90:10 %vol). We measured the rheological behaviour as a function of applied stress, σ, of suspensions at various volume fractions. We observed shear thickening behaviour, with divergences in the low-stress viscosity, η1(φ), and the high-stress viscosity, η2(φ), at φRCP = 0.662 and φm = 0.572 respectively. These divergences mark the transition between continuous shear thickening, discontinuous shear thickening and a state in which flow is not possible, with increasing volume fraction. Using a recently developed theory of shear thickening (Wyart and Cates, 2014), we were able to fit our rheological data quantitatively. The WC theory predicts a stress-dependent crossover in the fraction of contacts which are frictional in nature, following a stretched exponential function. In order to improve numerical agreement between our data and the model, we developed a method taking into
Multi-level cell STT-RAM: Is it realistic or just a dream?

Spin-transfer torque random access memory (STT-RAM) is a promising nonvolatile memory technology aiming on-chip or embedded applications. In recent years, many researches have been conducted to improve the storage density and enhance the scalability of STT-RAM, such as reducing the write current and switching time of magnetic tunneling junction (MTJ) devices. In parallel with these efforts, the continuous increasing of tunnel magneto-resistance(TMR) ratio of the MTJ inspires the development of multi-level cell (MLC) STT-RAM, which allows multiple data bits be stored in a single memory cell. Two types of MLC STT-RAM cells, namely, parallel MLC and series MLC, were also proposed. The storage margin of a MLC STT-RAM cell, i.e., the distinction between the lowest and highest resistance states, is partitioned into multiple segments for multi-level data representation. As a result, the performance and reliability of MLC STT-RAM cells become more sensitive to the MOS and MTJ device variations and the thermal-induced randomness of MTJ switching. In this work, we systematically analyze the variation sources of MLC STT-RAM designs and their impacts on the reliability of the read and write operations. On top of that, we also discuss the optimal device parameters of the MLC MTJ for the minimization of the operation error rate of the MLC STT-RAM cells from statistical design perspective. Our simulation results show that under the current available technology, series MLC STT-RAM demonstrates overwhelming benefits in the read and write reliability compared to parallel MLC STT-RAM and could potentially satisfy the requirement of commercial practices.
Host Targeted Activity of Pyrazinamide in Mycobacterium tuberculosis Infection

Pyrazinamide (PZA) is one of the first line antibiotics used for the treatment of tuberculosis (TB). In the present study, we have used in vitro and in vivo systems to investigate whether PZA, in addition to its known anti-mycobacterial properties, modulate the host immune response during Mycobacterium tuberculosis (Mtb) infection. In vitro we have examined the effect of PZA on cytokine and chemokine release by Mtb-infected or Toll-like receptor (TLR) -stimulated primary human monocytes. In vivo, we have investigated at the transcriptional levels using genome-wide microarray gene expression analysis, whether PZA treatment of Mtb-infected mice alters the host immune response to Mtb infection in the lungs. Here, we report that PZA treatment of Mtb-infected human monocytes and mice significantly reduces the release of pro-inflammatory cytokines and chemokines, including IL-1β, IL-6, TNF-α and MCP-1 at the protein and at the gene transcription levels, respectively. Data from microarray analysis also reveal that PZA treatment of Mtb-infected mice significantly alters the expression level of genes involved in the regulation of the pro-inflammatory mediators, lung inflammatory response and TLR signaling networks. Specifically, genes coding for adenylate cyclase and Peroxisome-Proliferator Activated Receptor (PPAR), molecules known for their anti-inflammatory effect, were found to be up-regulated in the lungs of PZA-treated Mtb-infected mice. Based on the microarray findings, we propose that PZA treatment modulates the host immune response to Mtb infection by reducing pro-inflammatory cytokine production, probably through PPAR- and NF-kB- dependent pathways. In addition, our results suggest that inclusion or exclusion of PZA in the TB treatment regimen could potentially affect the biomarker signature detected in the circulation of TB patients.
Dialectic: Enhancing Text Input Fields with Automatic Feedback to Improve Social Content Writing Quality

Modern social media relies on high quality user generated writing such as reviews, explanations, and answers. In contrast to standard validation to provide feedback for structured inputs (e.g., dates, email addresses), it is difficult to provide timely, high quality, customized feedback for free-form text input. While existing solutions based on crowdsourced feedback (e.g., up-votes and comments) can eventually produce high quality feedback, they suffer from high latency and costs, whereas fully automated approaches are limited to syntactic feedback that does not address text content. We introduce Dialectic, an end-to-end extensible system that simplifies the process of creating, customizing, and deploying content-specific feedback for free-text inputs. Our main observation is that many services already have a corpus of crowdsourced feedback that can be used to bootstrap a feedback system. Dialectic initializes with a corpus of annotated free-form text, automatically segments input text, and helps developers rapidly add domain-specific document quality features as well as content-specific feedback generation functions to provide targeted feedback to user inputs. Our user study shows that Dialectic can be used to create a feedback interface that produces an average of 14.4\% quality improvement of product review text, over 3x better than a state-of-the-art feedback system.
Characterization of Immortalized Human Corneal Endothelial Cell Line using HPV 16 E6/E7 on Lyophilized Human Amniotic Membrane

Purpose To establish the immortalized human corneal endothelial cell line (IHCEn) by transducing human papilloma virus (HPV) 16 E6/E7 oncogenes, and to identify their characteristics when cultivated on a lyophilized human amniotic membrane (LAM). Methods Primary human corneal endothelial cells (PHCEn) were infected using a retroviral vector with HPV 16 E6/E7, and transformed cells were clonally selected by G418. Growth properties and characteristics of IHCEn were compared with PHCEn by cell counting and RT-PCR of VDAC3, SLC4A4, CLCN3, FGF-1, Col IV, and Na+/K+ ATPase. IHCEn were cultured on LAM. Messenger RNA expressions of VDAC3, CLCN3, and Na+/K+ ATPase, and protein expressions of Na+/K+ ATPase and Col IV in IHCEn cultivated on LAM were investigated by RT-PCR, immunofluorescence, and immunohistochemical staining, respectively. Results Successful immortalization was confirmed by stable expression of HPV 16 E6/E7 mRNA by RT-PCR, and IHCEn exhibited typical corneal endothelial morphology. Doubling time of IHCEn was 30.15±10.96 hrs. Both IHCEn and PHCEn expressed VDAC3, CLCN3, SLC4A4, FGF-1, Col IV, and Na+/K+ ATPase. IHCEn cultivated on LAM showed stronger expression of VDAC3, CLCN4, and Na+/K+ ATPase mRNA than on plastic culture dish. Immunohistochemical staining and immunofluorescence revealed the positive expression of Na+/K+ ATPase and Col IV. Conclusions IHCEn were successfully established, and LAM is a good substrate for the culture of human corneal endothelial cells.