Miracle-dz/UniFAR-FTUs huggingface dataset:
Experimental Reconstruction of Functional Gene Transfer from the Tobacco Plastid Genome to the Nucleus[OA]

Eukaryotic cells arose through the uptake of free-living bacteria by endosymbiosis and their gradual conversion into organelles (plastids and mitochondria). Capture of the endosymbionts was followed by massive translocation of their genes to the genome of the host cell. How genes were transferred from the (prokaryotic) organellar genome to the (eukaryotic) nuclear genome and how the genes became functional in their new eukaryotic genetic environment is largely unknown. Here, we report the successful experimental reconstruction of functional gene transfer between an organelle and the nucleus, a process that normally occurs only on large evolutionary timescales. In consecutive genetic screens, we first transferred a chloroplast genome segment to the nucleus and then selected for gene activation in the nuclear genome. We show that DNA-mediated gene transfer can give rise to functional nuclear genes if followed by suitable rearrangements in the nuclear genome. Acquisition of gene function involves (1) transcriptional activation by capture of the promoter of an upstream nuclear gene and (2) utilization of AT-rich noncoding sequences downstream of the plastid gene as RNA cleavage and polyadenylation sites. Our results reveal the molecular mechanisms of how organellar DNA transferred to the nucleus gives rise to functional genes and reproduce in the laboratory a key process in the evolution of eukaryotic cells.
Mice Transgenic for IL-1 Receptor Antagonist Protein Are Resistant to Herpetic Stromal Keratitis: Possible Role for IL-1 in Herpetic Stromal Keratitis Pathogenesis1

Ocular infection with HSV may result in the blinding immunoinflammatory lesion stromal keratitis (SK). This represents a CD4+ T cell-mediated immunopathologic lesion in both humans and a mouse model. Early events in the pathogenesis that set the stage for SK are poorly understood. The present study evaluates the role of IL-1 using a transgenic mouse that overexpresses the IL-1 receptor antagonist (IL-1ra) protein. Such transgenic mice were markedly resistant to SK compared with IL-1ra−/− and C57BL/6 control animals. The resistance was shown to be the consequence of reduced expression of molecules such as IL-6, macrophage-inflammatory protein-2, and vascular endothelial growth factor, normally up-regulated directly or indirectly by IL-1. A critical event impaired in IL-1ra transgenic mice was vascular endothelial growth factor production with a consequent marked reduction in angiogenesis, an essential step in SK pathogenesis. Targeting IL-1 could prove to be a worthwhile therapeutic approach to control SK, an important cause of human blindness.
LiveSync: Deformed Viewing Spheres for Knowledge-Based Navigation

Although real-time interactive volume rendering is available even for very large data sets, this visualization method is used quite rarely in the clinical practice. We suspect this is because it is very complicated and time consuming to adjust the parameters to achieve meaningful results. The clinician has to take care of the appropriate viewpoint, zooming, transfer function setup, clipping planes and other parameters. Because of this, most often only 2D slices of the data set are examined. Our work introduces LiveSync, a new concept to synchronize 2D slice views and volumetric views of medical data sets. Through intuitive picking actions on the slice, the users define the anatomical structures they are interested in. The 3D volumetric view is updated automatically with the goal that the users are provided with expressive result images. To achieve this live synchronization we use a minimal set of derived information without the need for segmented data sets or data-specific pre-computations. The components we consider are the picked point, slice view zoom, patient orientation, viewpoint history, local object shape and visibility. We introduce deformed viewing spheres which encode the viewpoint quality for the components. A combination of these deformed viewing spheres is used to estimate a good viewpoint. Our system provides the physician with synchronized views which help to gain deeper insight into the medical data with minimal user interaction.
A Principled Approach to Distributed Multiscale Computing, from Formalization to Execution

In several disciplines, a multiscale approach is being used to model complex natural processes yet a principled background to multiscale modeling is not clear. Additionally, some multiscale models requiring distributed resources to be computed in an acceptable timeframe, while no standard framework for distributed multiscale computing is place. In this paper a principled approach to distributed multiscale computing is taken, formalizing multiscale modeling based on natural processes. Based on these foundations, the Multiscale Modeling Language (MML) is extended as a clear, general, formal, and high-level means to specify scales and interactions in, and as a guide to a uniform approach to crystalize, communicate, develop and execute a multiscale model. With an MML specification, a multiscale model can be analyzed for scheduling or deadlock detection using a task graph. The potential of this method is shown by applying it to two selected applications in nano materials and biophysics.
Use of communication technologies in romantic relationships

Self-disclosure is vital to the maintenance and development of personal relationships, but research regarding the use of communication technologies (CTs) for self-disclosure in relationships is mixed. This study extends previous research on the topic by examining associations between reduced-cue CT use, relationship development, and self-disclosure in specific conversations in proximal romantic relationships. Participants (N = 64) reported on each conversation with their partners over a 4-day period. Use of a reduced-cue CT in a conversation was negatively associated with self-disclosure breadth and depth in that conversation. Furthermore, the negative association between text-based CT use (text messaging, instant messaging, and e-mail) and self-disclosure breadth was weaker at higher levels of relationship development, and the negative association between voice-based CT use (telephone) and self-disclosure depth was stronger at higher levels of relationship development. These findings suggest that CTs function differently in proximal romantic relationships than in previous studies of interactions between strangers and that relationship development is an important factor in understanding self-disclosure via CTs.
Hearing Loss in Mitochondrial Disorders

Abstract: Hearing loss is a common clinical feature in mitochondria‐syndrome disorders. The underlining molecular etiology of hearing loss has not been fully investigated. In this study, 83 patients with mitochondrial syndromic hearing loss were evaluated clinically and their blood and tissue samples were examined molecularly. Using modified Walker's criteria, 31, 31, 14, and 7 patients had been classified as having definite, probable, possible, and unlikely diagnosis of mitochondrial disease, respectively. Deleterious mtDNA point mutations and/or abnormal mtDNA content or multiple deletions were identified in 20 patients with definite diagnosis and 2 patients with probable diagnosis. In addition to known, undisputed pathogenic mutations, several novel mutations believed to be clinically significant were found. Furthermore, abnormal mtDNA content and mtDNA deletions were found in some of the cases. Evaluation of clinical and diagnostic features associated with hearing loss revealed that cardiomyopathy, lactic acidosis, deficient respiratory chain enzyme complex activities, histochemical and ultrastructural abnormalities in mitochondria, and abnormal brain imaging results occurred significantly more frequently in patients with mtDNA alterations than in those without. This study revealed that the majority of the mtDNA defects in patients with mitochondrial syndromic hearing loss affect the overall mitochondrial gene expression.
79 GHz UWB automotive short range radar - Spectrum allocation and technology trends

Abstract. Automotive UWB (Ultra-Wideband) short range radar (SSR) is on the market as a key technology for novel comfort and safety systems. SiGe based 79 GHz UWB SRR will be a definite candidate for the long term substitution of the 24 GHz UWB SRR. This paper will give an overview of the finished BMBF joint project KOKON and the recently started successing project RoCC, which concentrate on the development of this technology and sensor demonstrators. In both projects, the responsibilities of Daimler AG deal with application based sensor specification, test and evaluation of realized sensor demonstrators. Recent UWB SRR frequency regulation approaches and activitites will be introduced. Furthermore, some first results of Daimler activities within RoCC will be presented, dealing with the packaging and operation of these sensors within the complex car environment.
Independent two-color optogenetic excitation of neural populations

The optical modulation of neurons with channelrhodopsins, a class of genetically encoded lightgated ion channels, has enabled the spatiotemporally precise interrogation of the roles individual cell types play in neural circuit dynamics. A topic of great interest to the neuroscience community is the independent optical excitation of two distinct neuron populations with different wavelengths, which would enable the interrogation of emergent phenomena such as circuit dynamics, plasticity, and neuromodulation. Previous implementations have focused on maximizing spectral separation by driving one channelrhodopsin in the violet (405 nm) and the other in the yellow (590 nm), yet it has not been possible to achieve independent violet excitation without eliciting spikes from both populations, due to the intrinsic UV-blue light sensitivity of the retinal chromophore. This thesis designs and implements an improved two-color excitation scheme where effective light sensitivity is utilized to achieve independent optical excitation in blue (470 nm) and red (625 nm) channels. Zero post-synaptic crosstalk is demonstrated in acute murine slice, using two novel channeirhodopsins identified from a systematic screen of 80 naturally occurring, previously uncharacterized opsins in primary neuron culture. Gene88 is the first known yellowpeaked channelrhodopsin, with a peak 45 nm more red-shifted than any previous channelrhodopsin, while Gene90 has the fastest channel turn on, turn off, and recovery kinetics of any known channelrhodopsin. These opsins' novel properties enable the first known demonstration of post-synaptic crosstalk-free two-color excitation with temporally precise modulation of spatially inseparable neuron populations.
The relationship between working memory and L2 reading comprehension

Since an important role for working memory has been found in the first language acquisition (e.g., Daneman, 1991; Daneman & Green, 1986; Waters & Caplan, 1996), research on the role of working memory is emerging as an area of concern for second language acquisition (e.g., Atkins & Baddeley, 1998; Miyake & Freidman, 1998; Robinson, 1995, 2002, 2005). The present study focused on the role of working memory capacity in the development of second language reading ability. 55 L1 Persian EFL learners at three proficiency levels from a private language school participated in this study. They completed a battery of reading and working memory measures. Memory measures included phonological short-term memory, and reading span test (RST). Reading measures included two expository reading comprehension tests. Multiple regression analysis was applied to determine whether there are any significant relationships between working memory capacity and reading measures. Results of this study indicated a significant relationship between working memory capacity (as measured by RST) and reading ability at lower levels of proficiency.
The Implementation of Teaching Speaking for Students with Hearing Impairment

e-mail: anggraeni.melina. ma@gmail.com Abstract The aim of this article is to report the result of a study about the implementation of teaching speaking for students with hearing impairment. Speaking as one of skills in using a foreign language is now necessary to be taught, including for the students with hearing impairment because of the effect of global competition nowadays. The method used in this research was descriptive qualitative method. The research was conducted at the eleventh grade students of SLB-B YPPALB Magelang academic year 2013/2014. The data were collected through the use of interview, observation, and document analysis. Based on the finding of this research, it can be concluded that: (1) the teacher has implemented the pre-activity, main activity, post activity and the evaluation based on the lesson plan made although he sometimes improves it according to the classroom condition, (2) There were 3 types of problems faced during the teaching-learning process which were students’ problem, the teacher’s problem and the problem on the school management, (3) there were some solutions proposed by the teacher to cope with those problems.
Newer antidepressants: a comparison of tolerability in general practice.

BACKGROUND An increasing number of antidepressants have been released on the United Kingdom market in recent years, and these are being prescribed more frequently in general practice. Clinical trials suggest that such agents have similar efficacy and the choice of drug is probably based on tolerability, toxicity in overdose, and cost. AIM To compare the tolerability and safety profile of six, newly marketed antidepressants used in general practice. METHOD Studies have been conducted for six antidepressants: fluoxetine, sertraline, paroxetine, moclobemide, venlafaxine, and nefazodone, using the technique of prescription-event monitoring. Patients were identified using incident dispensed prescription data. Questionnaires were sent to patients' general practitioners six months after the date of first prescription. Questionnaires asked for date of birth, sex, indication for prescribing each drug, and all events entered in the patients' records after the date of first prescription. RESULTS Each cohort exceeded 10,000 patients. Nausea/vomiting was the most frequently reported event for all drugs. The difference in incidence rates for drowsiness/sedation, male sexual dysfunction, and hypertension is shown. Mortality data are also reported. CONCLUSION Frequently reported events were similar for all six drugs but there were clinically and statistically significant differences for less frequently reported events. The adjusted mortality rate was identical between the six drugs. This study provides valuable comparative data for six, widely used antidepressants in general practice.
Typed open programming: a higher-order, typed approach to dynamic modularity and distribution

In this dissertation we develop an approach for reconciling open programming – the development of programs that support dynamic exchange of higher-order values with other processes – with strong static typing in programming languages. We present the design of a concrete programming language, Alice ML, that consists of a conventional functional language extended with a set of orthogonal features like higher-order modules, dynamic type checking, higher-order serialisation, and concurrency. On top of these a flexible system of dynamic components and a simple but expressive notion of distribution is realised. The central concept in this design is the package, a first-class value embedding a module along with its interface type, which is dynamically checked whenever the module is extracted. Furthermore, we develop a formal model for abstract types that is not invalidated by the presence of primitives for dynamic type inspection, as is the case for the standard model based on existential quantification. For that purpose, we present an idealised language in form of an extended λ-calculus, which can express dynamic generation of types. This calculus is the first to combine and explore the interference of sealing and type inspection with higher-order singleton kinds, a feature for expressing sharing constraints on abstract types. A novel notion of abstracton kinds classifies abstract types. Higher-order type and kind coercions allow for modular translucent encapsulation of values at arbitrary type.
High Precision and Large Range Timing Jitter Measurement and Control of Ultrashort Laser Pulses

An attosecond precision and femtosecond range timing jitter measurement and control technique is proposed. It is based on the modulation of the combined pulse induced by relative time delay of individual pulses. The core of this timing jitter detection method is the integrated technique of optical cross correlation and electrical energy interferometry. To illustrate this technique, a proof-of-principle experiment is demonstrated based on two 237 fs pulses. The peak-to-valley timing jitter of the two pulses to be combined is less than 700 as in 1 h and the average efficiency of coherent beam combining could reach to 91.6%.
Simulation-Based Performance Analysis of HSDPA for UMTS Networks

This paper investigates the performance of TCP over High Speed Downlink Packet Access (HSDPA) link in the third generation Universal Mobile Telecommunication System (UMTS). The throughput performance of TCP has been considered with both round robin and maximum carrier-tointerference scheduling schemes. A simulation based approach is adopted to determine the total cell throughput, both under ideal and Rayleigh fading conditions. Simulation results show that, HSDPA can effectively provide high throughputs, but with fairness depending upon the scheduling mechanism.
Perception of ethical climate and its relationship to nurses’ demographic characteristics and job satisfaction

In this study, we examined the perception of actual and ideal ethical climate type among 95 nurses working in the internal medicine wards of one central hospital in the state of Israel. We also examined whether nurses’ demographic characteristics influence that perception and if a relationship between perceptions of an actual and an ideal ethical climate type influences nurses’ job satisfaction. A questionnaire composed of three subquestionnaires was administered and the responses analyzed using multiple linear regressions, analysis of variance and Pearson’s correlation coefficient. The results demonstrated that demographic characteristics (such as: gender, job tenure and level of education) partially influence the perception of an ideal ethical climate. Incongruence in perceptions of ‘caring’ and ‘independence’ climate types indicated a decline in nurses’ job satisfaction, while perception of actual ‘caring’ and ‘service’ climates positively influenced all aspects of job satisfaction. We recommend constructing training programs emphasizing the ethics of nursing practice and also to help lead nurses to clarify an ethical framework and guide nursing staff in dealing with ethical dilemmas.
A Binary Deletion Channel With a Fixed Number of Deletions

Suppose a binary string x = x1 . xn is being broadcast repeatedly over a faulty communication channel. Each time, the channel delivers a fixed number m of the digits (m < n) with the lost digits chosen uniformly at random and the order of the surviving digits preserved. How large does m have to be to reconstruct the message?
Conversion of a bacterial warm sensor to a cold sensor by methylation of a single residue in the presence of an attractant

The aspartate chemoreceptor (Tar) of Escherichia coli also serves as a thermosensor, and it is very amenable to genetic and biochemical analysis of the thermosensing mechanism. Its thermosensing properties are controlled by reversible methylation of the cytoplasmic signalling/adaptation domain of the protein. The unmethylated and the fully methylated (aspartate‐bound) receptors sense, as attractant stimuli, increases (warm sensor) and decreases (cold sensor) in temperature respectively. To learn more about the mechanism of thermosensing, we replaced the four methyl‐accepting glutamyl residues with non‐methylatable aspartyl residues in all possible combinations. In a strain defective in both methyltransferase (CheR) and methylesterase (CheB) activities, all of the mutant Tar proteins functioned as warm sensors. To create a situation in which all of the remaining glutamyl residues were methylated, we expressed the mutant proteins in a CheB‐defective, CheR‐overproducing strain. The fully glutamyl‐methylated proteins were designed to mimic the full range of methylation states possible for wild‐type Tar. Almost all of the methylated mutant receptors, including those with single glutamyl residues, were cold sensors in the presence of aspartate. Thus, binding of aspartate to Tar and methylation of its single glutamyl residue can invert its temperature‐dependent signalling properties.
Stability of ribosomes of Staphylococcus aureus S6 sublethally heated in different buffers

Cells of Staphylococcus aureus heated at 52 degrees C in magnesium-chelating buffers [pH 7.2, 50 mM potassium phosphate or 50 mM tris(hydroxymethyl)-aminomethane containing 1 mM ethylenediaminetetraacetic acid] leaked 260-nm absorbing material, shown to be RNA, and suffered destruction of their ribosomes. These cells did not regain their salt tolerance when repair was carried out in the presence of actinomycin D (5 microgram/ml). Cells similarly heated in magnesium-conserving buffers [pH 7.2, 50 mM tris(hydroxymethyl)aminomethane containing 10 mM MgCl2 or piperazine buffer] did not leak RNA, suffered no ribosomal damage when heated for 15 min, and recovered, at least partially, in the presence of actinomycin D. Ribosomal damage, is therefore, a consequence of Mg2+ loss and is not an effect of heat per se. Cells suspended in either Mg2+-chelating or Mg2+-conserving buffers lost salt tolerance to about the same extent during heating at 52 degrees C. Therefore, sublethal heat injury can not be attributed to ribosomal damage.
Interpreting the Dependence of Mutation Rates on Age and Time

Mutations can originate from the chance misincorporation of nucleotides during DNA replication or from DNA lesions that arise between replication cycles and are not repaired correctly. We introduce a model that relates the source of mutations to their accumulation with cell divisions, providing a framework for understanding how mutation rates depend on sex, age, and cell division rate. We show that the accrual of mutations should track cell divisions not only when mutations are replicative in origin but also when they are non-replicative and repaired efficiently. One implication is that observations from diverse fields that to date have been interpreted as pointing to a replicative origin of most mutations could instead reflect the accumulation of mutations arising from endogenous reactions or exogenous mutagens. We further find that only mutations that arise from inefficiently repaired lesions will accrue according to absolute time; thus, unless life history traits co-vary, the phylogenetic “molecular clock” should not be expected to run steadily across species.
Nations: Old and new Comments on Anthony D. Smith's ‘The myth of the “Modern Nation” and the myths of nations’

Abstract Do common ethnicity and ethnic solidarity constitute preconditions for the successful formation of modern nations? In response to Anthony Smith's contention to this effect, it is here argued that ethnic solidarity at a large‐enough scale to constitute a nation is a problematic notion. Solidarities beyond small local communities require ideological and political underpinning. Rather than being preconditions of nation‐formation, ethnic homogeneity and solidarity are often products of a stable history of state and nation formation. The failures of some modern nation‐states with diverse ethnic compositions are an indication of inadequacy of resources for achieving stable ‘governability’.