Miracle-dz/UniFAR-FTUs huggingface dataset:
Breakthrough Technologies Positive Fluorescent Selection Permits Precise , Rapid , and In-Depth Overexpression Analysis in Plant Protoplasts 1

Transient genetic modification of plant protoplasts is a straightforward and rapid technique for the study of numerous aspects of plant biology. Recent studies in metazoan systems have utilized cell-based assays to interrogate signal transduction pathways using high-throughput methods. Plant biologists could benefit from new tools that expand the use of cell culture for large-scale analysis of gene function. We have developed a system that employs fluorescent positive selection in combination with flow cytometric analysis and fluorescence-activated cell sorting to isolate responses in the transformed protoplasts exclusively. The system overcomes the drawback that transfected protoplast suspensions are often a heterogeneous mix of cells that have and have not been successfully transformed. This Gateway-compatible system enables high-throughput screening of genetic circuitry using overexpression. The incorporation of a red fluorescent protein selection marker enables combined utilization with widely available green fluorescent protein (GFP) tools. For instance, such a dual labeling approach allows cytometric analysis of GFP reporter gene activation expressly in the transformed cells or fluorescence-activated cell sorting-mediated isolation and downstream examination of overexpression effects in a specific GFP-marked cell population. Here, as an example, novel uses of this system are applied to the study of auxin signaling, exploiting the red fluorescent protein/GFP dual labeling capability. In response to manipulation of the auxin response network through overexpression of dominant negative auxin signaling components, we quantify effects on auxin-responsive DR5TGFP reporter gene activation as well as profile genome-wide transcriptional changes specifically in cells expressing a root epidermal marker.
Nucleotide sequence of the rat low density lipoprotein receptor cDNA.

A 4.7 kb cDNA clone (ArLDL2-1a) coding for the rat low density lipoprotein (LDL) receptor was isolated from a Xgt-11 rat liver cDNA library (1,2). The DNA sequence of the entire coding region and portions of the 5' and 3' untranslated region is shown in Figure 1. The open reading frame coded for an 879 amino acid polypeptide with a theoretical molecular weight of 96,632, which is larger than the size ofthe human (3) and rabbit (4) LDL receptors. A signal sequence of 21 amino acids was also present in both the rat (Fig. 1) and human (3) receptors.
Surgical Clipping of Very Small Unruptured Intracranial Aneurysms: A Multicenter International Study.

BACKGROUND Treatment of very small unruptured intracranial aneurysms (VSUIAs, defined as ≤3 mm) can be indicated in selected circumstances. The feasibility and outcomes of endovascular therapy for VSUIAs have been recently published; however, the efficacy and complication rate of surgical clipping has not been reported in any large series to date. OBJECTIVE We conducted a multicenter study to examine surgical outcomes for VSUIAs. METHODS All consecutive patients undergoing surgery for a VSUIA in 4 neurosurgical centers between October 2001 and December 2012 were retrospectively analyzed. RESULTS In the study, 183 patients (128 women, mean age 51.3 years) were treated with 190 procedures for a total of 228 aneurysms. Most were anterior circulation aneurysms (n = 215). The majority were directly clipped (n = 222, 97.4%), with coagulation or wrapping in the remainder. After 1 reoperation for incomplete clipping, postoperative imaging of 225 aneurysms confirmed complete occlusion in 221 (98.2%), 1 neck remnant (0.44%), and 3 partial occlusions (1.3%). Mortality was 0%. Early postoperative neurological deficit developed in 12 patients (6.6%); posterior circulation location was a significant risk factor for early neurological deficit (P < .001). Middle cerebral artery aneurysms had the lowest rate of postoperative deficits at 1.5% (P = .023). After the initial 30-day perioperative period, all deficits related to treatment of posterior circulation aneurysms recovered; overall neurological morbidity decreased to 2.7% with no mortality. CONCLUSION VSUIA clipping is highly effective and is associated with a low morbidity rate. For VSUIAs selected for treatment, our data support surgical clipping as the modality of choice.
Definite Noun Phrases in Statistical Machine Translation into Scandinavian Languages

In this thesis I aim to improve phrase-based statistical machine translation (PBSMT) in a number of ways by the use of text harmonization strategies. PBSMT systems are built by training statistical models on large corpora of human translations. This architecture generally performs well for languages with similar structure. If the languages are different for example with respect to word order or morphological complexity, however, the standard methods do not tend to work well. I address this problem through text harmonization, by making texts more similar before training and applying a PBSMT system. I investigate how text harmonization can be used to improve PBSMT with a focus on four areas: compounding, definiteness, word order, and unknown words. For the first three areas, the focus is on linguistic differences between languages, which I address by applying transformation rules, using either rule-based or machine learning-based techniques, to the source or target data. For the last area, unknown words, I harmonize the translation input to the training data by replacing unknown words with known alternatives. I show that translation into languages with closed compounds can be improved by splitting and merging compounds. I develop new merging algorithms that outperform previously suggested algorithms and show how part-of-speech tags can be used to improve the order of compound parts. Scandinavian definite noun phrases are identified as a problem forPBSMT in translation into Scandinavian languages and I propose a preprocessing approach that addresses this problem and gives large improvements over a baseline. Several previous proposals for how to handle differences in reordering exist; I propose two types of extensions, iterating reordering and word alignment and using automatically induced word classes, which allow these methods to be used for less-resourced languages. Finally I identify several ways of replacing unknown words in the translation input, most notably a spell checking-inspired algorithm, which can be trained using character-based PBSMT techniques. Overall I present several approaches for extending PBSMT by the use of pre- and postprocessing techniques for text harmonization, and show experimentally that these methods work. Text harmonization methods are an efficient way to improve statistical machine translation within the phrase-based approach, without resorting to more complex models.
Long‐term T‐cell‐mediated immunity to epstein‐barr virus in man. I. Complete regression of virus‐induced transformation in cultures of seropositive donor leukocytes

Peripheral blood mononuclear cells from donors of known serological status with respect to EB virus were exposed to the virus in vitro and then cultured at various cell concentrations. All cultures from nine seronegative adult and 12 foetal donors gave rise to cell lines following subculture 4 weeks post infection. In contrast, seropositive donor cultures seeded at the higher cell concentrations developed foci of proliferating EBNA‐positive cells within the first 1–2 weeks but thereafter regressed completely and subcultures made after 4 weeks never gave rise to cell lines. Out of 18 seropositive donors tested, 15 showed regression in all cultures seeded at 106 cells/ml and above, and with the other three donors a proportion of replicate cultures regressed. T‐cell depletion and reconstitution experiments showed that the effect was absolutely dependent upon the presence in the cultures of T cells from these seropositive donors. The results strongly suggest that the regression phenomenon is an in vitro expression of long‐term T‐cell‐mediated immunity to EB virus which the large majority, if not all, infected individuals possess.
Microbial Communities Associated with Geological Horizons in Coastal Subseafloor Sediments from the Sea of Okhotsk

ABSTRACT Microbial communities from a subseafloor sediment core from the southwestern Sea of Okhotsk were evaluated by performing both cultivation-dependent and cultivation-independent (molecular) analyses. The core, which extended 58.1 m below the seafloor, was composed of pelagic clays with several volcanic ash layers containing fine pumice grains. Direct cell counting and quantitative PCR analysis of archaeal and bacterial 16S rRNA gene fragments indicated that the bacterial populations in the ash layers were approximately 2 to 10 times larger than those in the clays. Partial sequences of 1,210 rRNA gene clones revealed that there were qualitative differences in the microbial communities from the two different types of layers. Two phylogenetically distinct archaeal assemblages in the Crenarchaeota, the miscellaneous crenarchaeotic group and the deep-sea archaeal group, were the most predominant archaeal 16S rRNA gene components in the ash layers and the pelagic clays, respectively. Clones of 16S rRNA gene sequences from members of the gamma subclass of the class Proteobacteria dominated the ash layers, whereas sequences from members of the candidate division OP9 and the green nonsulfur bacteria dominated the pelagic clay environments. Molecular (16S rRNA gene sequence) analysis of 181 isolated colonies revealed that there was regional proliferation of viable heterotrophic mesophiles in the volcanic ash layers, along with some gram-positive bacteria and actinobacteria. The porous ash layers, which ranged in age from tens of thousands of years to hundreds of thousands of years, thus appear to be discrete microbial habitats within the coastal subseafloor clay sediment, which are capable of harboring microbial communities that are very distinct from the communities in the more abundant pelagic clays.
Multiple-antenna capacity in the low-power regime: channel knowledge and correlation

The capacity of multiple-antenna systems in the low-power regime has gained much attention recently (Lozano, A. et al., IEEE Trans. Information Theory, vol.49, no.10, p.2527-44, 2003). When two performance metrics, namely the minimum E/sub b//N/sub 0/ and the wideband slope, were studied, it turned out that antenna correlation and Rician factors do not have an impact on (E/sub b//N/sub 0/)/sub min/, but on the slope in bits/s/Hz/(3 dB). We analyze the impact of different types of CSI on the multiple-antenna capacity in the low-power regime. We show that (E/sub b//N/sub 0/)/sub min/ is reduced and the slope is increased by having channel knowledge at the transmit antenna array. The impact of spatial correlation on the two performance measures is completely characterized. Finally, the theoretical results are illustrated by numerical simulations showing the spectral efficiency over the received E/sub b//N/sub 0/ for various systems.
SYMMETRIZABLE FINITE DIFFERENCE OPERATORS

We introduce the notion of a symmetrizable finite difference oper- ator and prove that such operators are stable. We then present some sufficient conditions for symmetrizability. One of these extends H. -O. Kreiss' theorem on dissipative difference schemes for hyperbolic equations to a more general case with full (jc , invariable coefficients.
Diffusion of Innovative Health Care Services in the United States: A Study of Hospitals

A national sample of short-term hospitals is examined for differences in implementation of five innovative health programs. Findings are analyzed to differentiate the effects of selected demographic and organizational variables. Greater implementation is associated with large voluntary hospitals, hospitals located in metropolitan areas, and those located in the Northeastern states. Differential implementation patterns through time are shown to be well developed only for rehabilitation services. For all program areas, implementation rates approximate the normal diffusion curve.
Comparative study of task duplication static scheduling versus clustering and non-clustering techniques

One of the major issues that needs to be addressed in distributed memory multiprocessor (DMM) systems is the program task partitioning and scheduling problems, i.e. mapping of an application program's precedence related task threads among the processing elements of a DMM system. The optimal task partitioning and scheduling problem, with the goal of minimizing the program execution time and interprocessor communication overhead, is known to be an NP-complete problem. The paper addresses the design, development and performance evaluation of a novel static task partitioning and scheduling method called linear clustering with task duplication (LCTD). LCTD employs the linear (sequential) execution of tasks and task duplication heuristics in achieving minimized computation and interprocessor communication delays in DMMs. The superiority of the proposed LCTD algorithm is demonstrated through simulation studies and comparison against several of the existing static scheduling schemes, such as heavy node first (HNF) and linear clustering. We show that the proposed method can obtain an average of 33% improvement in program execution time and 21% improvement in processor utilization compared to linear clustering and HNF methods.
Electrochemical impedance study of fresh and passivated macroporous silicon for sensors

As-etched macroporous silicon layers were passivated successful by electrochemical oxidation and then covered by a chemically deposited polyaniline layer. They were studied by Fourier transform infrared spectroscopy (FTIR) and Impedance electrochemical spectroscopy (IES). The results show that electrochemical method is an excellent alternative for silicon oxide growth within the porous structure, whereas for polyaniline deposition into the insulating structure the chemical route is the most suitable. The FTIR analysis reveals that polyaniline in its emeraldine state, which is the most conductive one, was successful deposited into the porous matrix. The electrochemical behavior of these samples was studied by the impedance electrochemical spectroscopy (IES) and shows that IES is sensitive to surface chemical properties variation at the film/electrolyte interface, as well as to the chemical composition of the electrolyte. The addition of low amounts of contaminants, in the order of ppb, promotes a shift of its real and imaginary impedance, showing that these samples can be used as excellent chemosensor for contaminants in ethanoic solution.
ParkUs: A Novel Vehicle Parking Detection System

Finding on-street parking in congested urban areas is a challenging chore that most drivers worldwide dislike. Previous vehicle traffic studies have estimated that around thirty percent of vehicles travelling in inner city areas are made up of drivers searching for a vacant parking space. While there are hardware sensor based solutions to monitor on-street parking occupancy in real-time, instrumenting and maintaining such a city wide system is a substantial investment. In this paper, a novel vehicle parking activity detection method, called ParkUs, is introduced and tested with the aim to eventually reduce vacant car parking space search times. The system utilises accelerometer and magnetometer sensors found in all smartphones in order to detect parking activity within a city environment. Moreover, it uses a novel sensor fusion feature called the Orthogonality Error Estimate (OEE). We show that the OEE is an excellent indicator as it’s capable of detecting parking activities with high accuracy and low energy consumption. One of the envisioned applications of the ParkUs system will be to provide all drivers with guidelines on where they are most likely to find vacant parking spaces within a city. Therefore, reducing the time required to find a vacant parking space and subsequently vehicle congestion and emissions within the city.
Retirement Choices in Italy: What an Option Value Model Tells Us

Using Italian data, we estimate an option value model to quantify the effect of financial incentives on retirement choices. As far as we know, this is the first empirical study to estimate the conditional multiple-years model put forward by Stock and Wise (1990). This implies that we account for dynamic self-selection bias. We also present an extended version of this model in which the marginal value of leisure is random. The models yield plausible estimates of the preference parameters. Dynamic self-selection results in a considerable downward bias in the estimate of the marginal utility of leisure. We perform a simulation study to gauge the effects of a dramatic pension reform. Underestimation of the value of leisure translates into sizeable over-prediction of the impact of reform. For the female sample, the model is able to predict almost perfectly the age-specific hazard rates. For the male sample, we obtain a good fit. Results for males should, however, be interpreted with caution since we are not able to fully correct for dynamic self-selection bias.
Experimental demonstration of dynamic focusing of a relativistic electron bunch by an overdense plasma lens.

Dynamic focusing of a 3.8 MeV electron bunch, a few collisionless skin depths long \ensuremath{\sim}3c/${\mathrm{\ensuremath{\omega}}}_{\mathit{p}}$, by an overdense, thick plasma lens has been demonstrated. Because of electron inertial effects, the head of the bunch is virtually unaffected by the lens while the rest is focused to varying degree. Time-resolved measurements performed 31 cm downstream of the plasma lens show that, in time, the bunch pinches from an initial size of 2.7 mm (FWHM) to about 0.57 mm and then expands, in reasonable agreement with theory.
Disruption of the SRC-1 gene in mice suppresses breast cancer metastasis without affecting primary tumor formation

Steroid receptor coactivator-1 (SRC-1) is a coactivator for nuclear hormone receptors such as estrogen and progesterone receptors and certain other transcription factors such as Ets-2 and PEA3. SRC-1 expression in breast cancer is associated with HER2 and c-Myc expression and with reduced disease-free survival. In this study, SRC-1−/− mice were backcrossed with FVB mice and then cross-bred with MMTV-polyoma middle T antigen (PyMT) mice to investigate the role of SRC-1 in breast cancer. Although mammary tumor initiation and growth were similar in SRC-1−/−/PyMT and wild-type (WT)/PyMT mice, genetic ablation of SRC-1 antagonized PyMT-induced restriction of mammary ductal differentiation and elongation. SRC-1−/−/PyMT mammary tumors were also more differentiated than WT/PyMT mammary tumors. The intravasation of mammary tumor cells and the frequency and extent of lung metastasis were drastically reduced in SRC-1−/−/PyMT mice compared with WT/PyMT mice. Metastatic analysis of transplanted WT/PyMT and SRC-1−/−/PyMT tumors in SRC-1−/− and WT recipient mice revealed that SRC-1 played an intrinsic role in tumor cell metastasis. Furthermore, SRC-1 was up-regulated during mammary tumor progression. Disruption of SRC-1 inhibited Ets-2-mediated HER2 expression and PyMT-stimulated Akt activation in the mammary tumors. Disruption of SRC-1 also suppressed colony-stimulating factor-1 (CSF-1) expression and reduced macrophage recruitment to the tumor site. These results suggest that SRC-1 specifically promotes metastasis without affecting primary tumor growth. SRC-1 may promote metastasis through mediating Ets-2-mediated HER2 expression and activating CSF-1 expression for macrophage recruitment. Therefore, functional interventions for coactivators like SRC-1 may provide unique approaches to control breast cancer progression and metastasis.
The Herpes Simplex Virus 1 UL34 Protein Interacts with a Cytoplasmic Dynein Intermediate Chain and Targets Nuclear Membrane

ABSTRACT To express the function encoded in its genome, the herpes simplex virus 1 capsid-tegument structure released by deenvelopment during entry into cells must be transported retrograde to the nuclear pore where viral DNA is released into the nucleus. This path is essential in the case of virus entering axons of dorsal root ganglia. The objective of the study was to identify the viral proteins that may be involved in the transport. We report the following findings. (i) The neuronal isoform of the intermediate chain (IC-1a) of the dynein complex pulled down, from lysates of [35S]methionine-labeled infected cells, two viral proteins identified as the products of UL34 and UL31 open reading frames, respectively. UL34 protein is a virion protein associated with cellular membranes and phosphorylated by the viral kinase US3. UL31 protein is a largely insoluble, evenly dispersed nuclear phosphoprotein required for optimal processing and packaging of viral DNA into preformed capsids. Reciprocal pulldown experiments verified the interaction of IC-1a and UL34 protein. In similar experiments, UL34 protein was found to interact with UL31 protein and the major capsid protein ICP5. (ii) To determine whether UL34 protein is transported to the nuclear membrane, a requirement if it is involved in transport, the UL34 protein was inserted into a baculovirus vector under the cytomegalovirus major early promoter. Cells infected with the recombinant baculovirus expressed UL34 protein in a dose-dependent manner, and the UL34 protein localized primarily in the nuclear membrane. An unexpected finding was that UL34-expressing cells showed a dissociation of the inner and outer nuclear membranes reminiscent of the morphologic changes seen in cells productively infected with herpes simplex virus 1. UL34, like many other viral proteins, may have multiple functions expressed both early and late in infection.
The Childhood Cancer Survivor Study-Neurocognitive Questionnaire (CCSS-NCQ) revised: item response analysis and concurrent validity.

OBJECTIVE Childhood cancer survivors are at risk for neurocognitive impairment related to cancer diagnosis or treatment. This study refined and further validated the Childhood Cancer Survivor Study-Neurocognitive Questionnaire (CCSS-NCQ; Krull et al., 2008), a scale developed to screen for impairment in long-term survivors of childhood cancer. METHOD Items related to task efficiency, memory, organization, and emotional-regulation domains were examined using item response theory (IRT). Data were collected from 833 adult survivors of childhood cancer who completed self-report and direct neurocognitive testing for the St. Jude Lifetime Cohort Study. The revision process included: (a) content-validity mapping of items to domains, (b) constructing a revised CCSS-NCQ, (c) selecting items within specific domains using IRT, and (d) evaluating concordance between the revised CCSS-NCQ and direct neurocognitive assessment. RESULTS Using content and measurement properties, 32 items were retained (8 items in 4 domains). Items captured low to middle levels of neurocognitive concerns. The latent domain scores demonstrated poor convergent/divergent validity with the direct assessments. Adjusted ESs (ES; Cohen's d) for agreement between self-reported memory and direct memory assessment were moderate for total recall (ES = 0.66), long-term memory (ES = 0.63), and short-term memory (STM; ES = 0.55). ESs between self-rated task efficiency and direct assessment of attention were moderate for focused attention (ES = 0.70) and attention span (ES = 0.50), but small for sustained attention (ES = 0.36). Cranial radiation therapy and female gender were associated with lower self-reported neurocognitive function. CONCLUSION The revised CCSS-NCQ demonstrates adequate measurement properties for assessing day-to-day neurocognitive concerns in childhood cancer survivors, and adds useful information to direct assessment.