Miracle-dz/UniFAR-FTUs huggingface dataset:
Bioinformatics TrichOME : A Comparative Omics Database for Plant Trichomes 1

Plant Biology Division, The Samuel Roberts Noble Foundation, Ardmore, Oklahoma 73401 (X.D., D.S.Y., Y.T., L.W.S., R.A.D., P.X.Z.); Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China (G.W.); Nestlé R&D Center Tours, Plant Science and Technology, 37390 Notre-Dame D’Oé, France (P.B.); and Department of Plant Biology, University of Minnesota, St. Paul, Minnesota 55108 (M.D.M.)
Immunodominant Semen Proteins III: IgG 1 and IgG 4 Linkage in Female Immune Infertility

Active immune mechanism in the female reproductive tract may produce high levels of anti-seminal/sperm antibodies. Generated antibodies in the process of isoimmunization seem to be associated with female immune infertility. The aim of our study consists in the profiling of specific serum immunoglobulin classes and subclasses in infertile women. We focus on the distribution of serum seminal/sperm-specific antibodies in order to find those apparently related to female isoimmunization. Immunoglobulins G1-4, A1,2, M and E were measured by ELISA in serum from 30 infertile and 10 fertile females. Anti-seminal/sperm IgG1 and IgG4 fractions were predominantly detected. Anti-seminal IgG1 and IgG4 were observed approximately in the 2:1 ratio, anti-sperm fraction in the 1:2 ratio. Strikingly, the approximate ratio between IgG1 and IgG2 was 3:1 in seminal specific and 2:1 in sperm specific antibodies. Surprisingly, IgG3 antibodies were nearly negative for both antigen fractions, seminal and sperm. Concerning our results, the proportionality does exist between seminal and sperm antibody fractions. Based on the poorly detectable levels of semen specific IgE, M, A1,2, G3, the markers of pathologic female isoimmunization appear to be the serum IgG1 and IgG4. These preliminary findings may contribute to a detailed patient diagnosis and an improved therapy.
Research on Evaluation System for Project Success

Research on project success is an eternal issue in project management. It has very important meaning in current social and economical innovation in China. Establishment of reasonable evaluation system can not only deepen cognition of the partner, but also used as reference to the establishment of controlling system of the subsequent project. This paper established longitudinal and lateral evaluation system based on DEA and three-hierarchy analysis of effect. Results indicated that the evaluation value could be divided into six regions and the regions could be generalized as four types, they are optimization region, permissible region, improvement needed region and impermissible regions. Improvement directions were pointed out aim to some regions.
Three Cases Illustrating the Presence of Argentaffin (Kultschitzky) Cells in the Human Gall-bladder

Occasionally typical argentaffin (Kultschitzky) cell or so-called "carcinoid " tumours have been described in the human gall-bladder (Joel, 1929; Porter and Whelan, 1939; Bosse, 1943), although I have found no mention in textbooks of histology or pathology of the presence of such cells in the mucosa. There is, however, one case report (Kerr and Lendrum, 1936) of a papilloma of this organ covered with intestinal epithelium containing both Paneth and argentaffin cells. I propose to describe three cases in which the latter type was present.
Experimental Investigation of LP11 Mode to OAM Conversion in Few Mode-Polarization Maintaining Fiber and the Usage for All Fiber OAM Generator

In this paper, the LP<sub>11</sub> mode evolution in a few mode-polarization maintaining fiber is experimentally investigated. Selective conversion from the LP<sub>11</sub>a/LP<sub>11</sub>b mode to the LP<sub>11</sub>b/LP<sub>11</sub>a , OAM<sub>+1</sub>, and OAM<sub>-1</sub> modes are demonstrated with varying wavelengths and fiber lengths. This property may have nice applications in spatial division multiplexing (SDM) systems, and one of them, i.e., the all-fiber compact and robust scalar orbital angular momentum (OAM) generator, which is cascaded by a mode-selective coupler and a few mode-polarization maintaining fiber, is also demonstrated with expected performance for conversion between LP<sub>01</sub> mode and OAM<sub>+1</sub>/OAM<sub>-1</sub>.
Manifold regularized non-negative matrix factorization with label information

Abstract. Non-negative matrix factorization (NMF) as a popular technique for finding parts-based, linear representations of non-negative data has been successfully applied in a wide range of applications, such as feature learning, dictionary learning, and dimensionality reduction. However, both the local manifold regularization of data and the discriminative information of the available label have not been taken into account together in NMF. We propose a new semisupervised matrix decomposition method, called manifold regularized non-negative matrix factorization (MRNMF) with label information, which incorporates the manifold regularization and the label information into the NMF to improve the performance of NMF in clustering tasks. We encode the local geometrical structure of the data space by constructing a nearest neighbor graph and enhance the discriminative ability of different classes by effectively using the label information. Experimental comparisons with the state-of-the-art methods on theCOIL20, PIE, Extended Yale B, and MNIST databases demonstrate the effectiveness of MRNMF.
Generalized Degrees of Freedom of the Symmetric Cache-Aided MISO Broadcast Channel With Partial CSIT

We consider the cache-aided MISO broadcast channel (BC) in which a multi-antenna transmitter serves $K$ single-antenna receivers, each equipped with a cache memory. The transmitter has access to partial knowledge of the channel state information. For a symmetric setting, in terms of channel strength levels, partial channel knowledge levels and cache sizes, we characterize the generalized degrees of freedom (GDoF) up to a constant multiplicative factor. The achievability scheme exploits the interplay between spatial multiplexing gains and coded-multicasting gain. On the other hand, a cut-set-based argument in conjunction with a GDoF outer bound for a parallel MISO BC under channel uncertainty is used for the converse. We further show that the characterized order-optimal GDoF is also attained in a decentralized setting, where no coordination is required for content placement in the caches.
Color-based hands tracking system for sign language recognition

The paper describes a real-time system which tracks the uncovered/unmarked hands of a person performing sign language. It extracts the face and hand regions using their skin colors, computes blobs and then tracks the location of each hand using a Kalman filter. The system has been tested for hand tracking using actual sign-language motion by native signers. The experimental results indicate that the system is capable of tracking hands even while they are overlapping the face.
Identification and Molecular Analysis of Rough-Colony-Specific Outer Membrane Proteins of Actinobacillus actinomycetemcomitans

ABSTRACT Actinobacillus actinomycetemcomitans, a gram-negative bacterium isolated from the human mouth, has been implicated in the pathogenesis of early-onset periodontitis. Primary isolates cultured from subgingival plaque exhibit an adherent, rough colony phenotype which spontaneously converts to a nonadherent, smooth phenotype upon in vitro subculture. The rough colony variant produces abundant fimbriae and autoaggregates, while the smooth colony variant is planktonic and produces scant fimbriae. To begin to understand the significance of colony variation in biofilm formation by A. actinomycetemcomitans, outer membrane protein profiles of four isogenic rough and smooth colony variants were compared by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. Two proteins with relative molecular masses of 43 and 20 kDa were expressed by the rough colony variants exclusively. Expression of these proteins was not found to be dependent on growth phase, oxygen tension, or type of complex medium. N-terminal amino acid sequences of these proteins obtained by Edman degradation were compared with sequences from the University of Oklahoma A. actinomycetemcomitans genome database. Two contiguous open reading frames (ORFs) encoding proteins having sequence homology with these proteins were identified. The 43-kDa protein (RcpA [rough colony protein A]) was similar to precursor protein D of the general secretion pathway of gram-negative bacilli, while the 20-kDa protein (RcpB [rough colony protein B]) appeared to be unique. The genes encoding these proteins have been cloned from A. actinomycetemcomitans 283 and sequenced. A BLASTX (gapped BLAST) search of the surrounding ORFs revealed homology with other fimbria-related proteins. These data suggest that the genes encoding the 43-kDa (rcpA) and 20-kDa (rcpB) proteins may be functionally related to each other and to genes that may encode fimbria-associated proteins.
Sustaining Educational Reforms in Introductory Physics.

While it is well known which curricular practices can improve student performance on measures of conceptual understanding, the sustaining of these practices and the role of faculty members in implementing these practices are less well understood. We present a study of the hand-off of Tutorials in Introductory Physics from initial adopters to other instructors at the University of Colorado, including traditional faculty not involved in physics education research. The study examines the impact of implementation of Tutorials on student conceptual learning across eight first-semester, and seven second-semester courses, for fifteen faculty over twelve semesters, and includes roughly 4000 students. It is possible to demonstrate consistently high, and statistically indistinguishable, student learning gains for different faculty members; however, such results are not the norm, and appear to rely on a variety of factors. Student performance varies by faculty background - faculty involved in, or informed by physics education research, consistently post higher student learning gains than less-informed faculty. Student performance in these courses also varies by curricula used - all semesters in which the research-based Tutorials and Learning Assistants are used have higher student learning gains than those semesters that rely on non-research based materials and do not employ Learning Assistants.
Association of c‐fos mRNA expression and excitotoxicity in primary cultures of mouse neocortical and cerebellar neurons

The effect of excitatory amino acids (EAAs) on c‐fos mRNA expression was studied in primary cultures of mouse cerebellar granule cells and in neocortical neurons after 2 and 7 days in vitro (div). In cultured granule cells at 2 and 7 div, and in cortical neurons at 2 div, exposure to low levels (≤10 μM) of a variety of EAAs (viz. glutamate [Glu], S‐sulpho‐L‐cysteine [SC], N‐methyl‐D‐aspartate [NMDA], α‐amino‐3‐hydroxy‐5‐methyl‐4‐isoxazole [AMPA], and kainate [KA]) resulted in a transient increase in the level of c‐fos mRNA which peaked at 30 min but returned to a basal level by 120 min. However, exposure of granule cells (7 div) to high levels (250 μM) of Glu, NMDA, KA, SC and of cortical neurons (7 div) to high levels (250 μM) of Glu, NMDA, KA, SC, or AMPA and to low levels (≤10 μM) of Glu and AMPA resulted in a delay in c‐fos mRNA induction but a subsequent, progressive increase that was sustained for at least 240 min. Furthermore, this effect was accompanied by a dose‐related increase in the release of the cytosolic enzyme, lactate dehydrogenase, used as an indicator of excitotoxicity. A ratio (Q240/30) for the steady‐state levels of c‐fos mRNA after 30 min and 240 min of exposure to EAAs was determined which showed that Q240/30 >2 correlated reproducibly with excitotoxic cell death, whereas a ratio of ≤1 correlated with a nonexcitotoxic event. In both cell types at 7 div, coadministration of the selective NMDA receptor antagonist, DL(±)‐2‐amino‐5‐phosphonopentanoic acid (APV) with cytotoxic levels of Glu 1) protected against EAA‐induced neurotoxicity and 2) exhibited a transient c‐fos mRNA expression (Q240/30 values ≈1). In contrast, the AMPA/KA receptor antagonist, 6‐cyano‐7‐nitroquinoxaline‐2,3‐dione (CNQX), provided no protection against excitotoxicity and had no significant effect on the Glu‐induced delay in c‐fos mRNA expression. These results suggest that the Q240/30 c‐fos mRNA ratio may 1) be used as a predictive index for excitotoxic neuronal death, 2) provide information on the identity of the receptor subtype mediating excitotoxicity in different brain cell types, and 3) aid in establishing the role of excitotoxicity during the development of neurons in vitro. J. Neurosci. Res. 48:533–542, 1997. © 1997 Wiley‐Liss Inc.
A multi-physics approach for the analysis and design of optomechanical cavities

In this contribution, we report on numerical simulation of a multi-physic Electromagnetic/Mechanical problem, as a further step towards the development of GHz circuits based on phonon propagation at micro-and nano-scale. In the future, this kind of circuits is likely to integrate optomechanically pumped phonon sources and detectors, as well as phonon processing components (waveguides, splitters, memories) to process information by means of phonons. In particular, we propose a rigorous approach for the solution of the electromagnetic/mechanical system of equations governing light behavior in opto-mechanical cavities, with the help of the Transformation Optics (TO) method. Such kind of calculation allows the development of an efficient generation of GHz to tens of GHz coherent phonon sources, by engineering their propagation or coupling with phonon waveguides.
Association Between Index Hospitalization and Hospital Readmission in Sepsis Survivors*

Objectives:Hospital readmission is common after sepsis, yet the relationship between the index admission and readmission remains poorly understood. We sought to examine the relationship between infection during the index acute care hospitalization and readmission and to identify potentially modifiable factors during the index sepsis hospitalization associated with readmission. Design:In a retrospective cohort study, we evaluated 444 sepsis survivors at risk of an unplanned hospital readmission in 2012. The primary outcome was 30-day unplanned hospital readmission. Setting:Three hospitals within an academic healthcare system. Subjects:Four hundred forty-four sepsis survivors. Measurements and Main Results:Of 444 sepsis survivors, 23.4% (95% CI, 19.6–27.6%) experienced an unplanned 30-day readmission compared with 10.1% (95% CI, 9.6–10.7%) among 11,364 nonsepsis survivors over the same time period. The most common cause for readmission after sepsis was infection (69.2%, 72 of 104). Among infection-related readmissions, 51.4% were categorized as recurrent/unresolved. Patients with sepsis present on their index admission who also developed a hospital-acquired infection (“second hit”) were nearly twice as likely to have an unplanned 30-day readmission compared with those who presented with sepsis at admission and did not develop a hospital-acquired infection or those who presented without infection and then developed hospital-acquired sepsis (38.6% vs 22.2% vs 20.0%, p = 0.04). Infection-related hospital readmissions, specifically, were more likely in patients with a “second hit” and patients receiving a longer duration of antibiotics. The use of total parenteral nutrition (p = 0.03), longer duration of antibiotics (p = 0.047), prior hospitalizations, and lower discharge hemoglobin (p = 0.04) were independently associated with hospital readmission. Conclusions:We confirmed that the majority of unplanned hospital readmissions after sepsis are due to an infection. We found that patients with sepsis at admission who developed a hospital-acquired infection, and those who received a longer duration of antibiotics, appear to be high-risk groups for unplanned, all-cause 30-day readmissions and infection-related 30-day readmissions.
Subtle features of ice with cloudy effects and scratches from collision damage

We propose a simulation framework for expressing cloudy effects and scratches on ice caused by the collision of other objects. Cloudy effects are created and diffused in proportion to the collision on the ice surfaces calculated by a combination of a grid‐projection technique and the boundary particle method. To prevent dissipation during the diffusion process, a geodesic distance is used as a constraint. Scratches are modeled directionally by analyzing the density gradient of cloudy effects and rendered using needle‐shaped ellipsoids. Experiments provide detailed expression of cloudy effects and scratches from collision damage. Copyright © 2016 John Wiley & Sons, Ltd.
Interstitial capillary changes in lithium nephropathy: effects of antihypertensive treatment

Histopathological changes were investigated in the tubulointerstitium and in the capillaries of male Wistar rats with lithium‐induced nephropathy using stereological methods. Two antihypertensive drugs with opposite effects on the renin‐angiotensin system, an ACE inhibitor (angiotensin converting enzyme inhibitor) and a thiazide diuretic, modified the nephropathy. Generally, there was a significant positive correlation between the reduction in GFR (glomerular filtration rate) and the reduction in the volume of intact tubular structures and interstitial capillaries. A significant negative correlation was seen between the reduction in GFR and the increase in tubulocapillary distance and the absolute volume of interstitial connective tissue, respectively. Treatment with perindopril, and to some extent hydrochlorothiazide, reversed the rise in systolic blood pressure associated with lithium‐induced nephropathy but did not affect the progression to terminal uraemia, the structural renal changes or the mortality. In conclusion, severe tubular and capillary changes are seen in this model of chronic renal failure. Tubular atrophy is associated with a decrease in interstitial capillaries and with an increase in the tubulocapillary distance. Systemic hypertension or activation of the renin‐angiotensin system may not be important factors for the progression to terminal renal failure.
Xylella fastidiosa outer membrane vesicles modulate plant colonization by blocking attachment to surfaces

Significance Release of outer membrane vesicles (OMVs) is a general feature of Gram-negative bacteria. Most studies have addressed the mechanisms of their formation or the cargo they can carry, but other roles remain to be explored further. Here we provide evidence for a novel role for OMVs in Xylella fastidiosa, a bacterial pathogen that colonizes the xylem of important crop plants. OMVs, whose production is suppressed by a quorum-sensing system, serve as an autoinhibitor of cell adhesion to surfaces, thereby blocking attachment-driven biofilm formation that would restrict movement within the xylem and thus colonization of plants. The ubiquity of OMV formation in the bacterial world suggests that these extracellular products may have alternative roles that might modulate movement and biofilm formation. Outer membrane vesicles (OMVs) of Gram-negative bacteria have been studied intensively in recent years, primarily in their role in delivering virulence factors and antigens during pathogenesis. However, the near ubiquity of their production suggests that they may play other roles, such as responding to envelope stress or trafficking various cargoes to prevent dilution or degradation by other bacterial species. Here we show that OMVs produced by Xylella fastidiosa, a xylem-colonizing plant pathogenic bacterium, block its interaction with various surfaces such as the walls of xylem vessels in host plants. The release of OMVs was suppressed by the diffusible signal factor-dependent quorum-sensing system, and a X. fastidiosa ΔrpfF mutant in which quorum signaling was disrupted was both much more virulent to plants and less adhesive to glass and plant surfaces than the WT strain. The higher virulence of the ΔrpfF mutant was associated with fivefold higher numbers of OMVs recovered from xylem sap of infected plants. The frequency of attachment of X. fastidiosa to xylem vessels was 20-fold lower in the presence of OMVs than in their absence. OMV production thus is a strategy used by X. fastidiosa cells to adjust attachment to surfaces in its transition from adhesive cells capable of insect transmission to an “exploratory” lifestyle for systemic spread within the plant host which would be hindered by attachment. OMV production may contribute to the movement of other bacteria in porous environments by similarly reducing their contact with environmental constituents.
Joint Modeling of the Clinical Progression and of the Biomarkers' Dynamics Using a Mechanistic Model

Summary Joint models are used to rigorously explore the relationship between the dynamics of biomarkers and clinical events. In the context of HIV infection, where the multivariate dynamics of HIV‐RNA and CD4 are complex, a mechanistic approach based on a system of nonlinear differential equations naturally takes into account the correlation between the biomarkers. Using data from a randomized clinical trial comparing dual antiretroviral therapy to a single drug regimen, a full maximum likelihood approach is proposed to explore the relationship between the evolution of the biomarkers and the time to a clinical event. The role of each marker as an independent predictor of disease progression is assessed. We show that the joint dynamics of HIV‐RNA and CD4 captures the effect of antiretroviral treatment; the CD4 dynamics alone is found to capture most but not all of the treatment effect.
Functional Disability Profiles in Amnestic Mild Cognitive Impairment

Background/Aims: Instrumental activities of daily living (IADL) can be impaired in mild cognitive impairment (MCI), and the severity of functional disability predicts Alzheimer’s disease (AD) in amnestic MCI (aMCI). This study investigated the functional profiles of aMCI in a Chinese population. Methods: The Disability Assessment for Dementia scores of 56 subjects with single-domain aMCI (sd-aMCI) and 94 with multiple-domain aMCI (md-aMCI) were compared with normal controls (n = 64) and mild AD patients (n = 102). Results: Both the sd-aMCI (2.5 ± 2.5) and md-aMCI (3.7 ± 3.5) groups had more impaired IADL items than the controls (0.7 ± 1.7). Their IADL scores were intermediate, between the control and AD groups. sd-aMCI subjects presented deficits in 7 IADL items involving the ‘meal preparation’, ‘telephoning’, ‘finance’, ‘medications’, ‘housework’, and ‘leisure’ subscales. md-aMCI subjects presented deficits in 14 IADL items involving all subscales of daily activities. The Mini-Mental State Examination and Modified Trail-Making Test Part B scores were the major neuropsychological correlates of IADL performance in aMCI. Conclusion: IADL can be impaired in both sd-aMCI and md-aMCI. Including the functional ability assessment in the evaluation of aMCI may help clinicians to provide appropriate suggestions to maintain daily functioning.