Miracle-dz/UniFAR-FTUs huggingface dataset:
Precision instrument placement using a 4-DOF robot with integrated fiducials for minimally invasive interventions

Minimally invasive procedures are increasingly attractive to patients and medical personnel because they can reduce operative trauma, recovery times, and overall costs. However, during these procedures, the physician has a very limited view of the interventional field and the exact position of surgical instruments. We present an image-guided platform for precision placement of surgical instruments based upon a small four degree-of-freedom robot (B-RobII; ARC Seibersdorf Research GmbH, Vienna, Austria). This platform includes a custom instrument guide with an integrated spiral fiducial pattern as the robot's end-effector, and it uses intra-operative computed tomography (CT) to register the robot to the patient directly before the intervention. The physician can then use a graphical user interface (GUI) to select a path for percutaneous access, and the robot will automatically align the instrument guide along this path. Potential anatomical targets include the liver, kidney, prostate, and spine. This paper describes the robotic platform, workflow, software, and algorithms used by the system. To demonstrate the algorithmic accuracy and suitability of the custom instrument guide, we also present results from experiments as well as estimates of the maximum error between target and instrument tip.
Dynamic variations in bark hydraulics - understanding whole tree processes and its linkage to bark hydraulic function and structure

A mature tree stem generally consists of a column of wood that is composed of a series of annual incremental layers and enclosed in a covering of bark. The dynamic variations of the bark are complex due to its structure and function: the thick outer-bark acts as a protective barrier against the abiotic and biotic environment; while the phloem is where sugar transport occurs. Much of the bark variation is due to the transport of sugars and its related processes. The driving force for sugar transport in the phloem is generated by the accumulation of sugars at source sites (e.g. leaves), which creates differences in gradients in turgor pressure along the stem. As a result, mass flow occurs – transporting sugars to sink regions that require it (e.g. stem and roots) for active growth, respiration and storage. The xylem pathway, which transports water in the opposite direction, is connected to the phloem in parallel along the entire length of the stem. The immediate connection between these two transport pathways suggests a functional linkage, as the phloem draws water from the xylem in order for mass flow to occur. The dynamic interactions between the xylem and phloem, and the processes occurring within the bark have great implications for whole tree physiology. The purpose of this thesis is to study the dynamic processes that occur within the bark and its interaction with other internal tree processes and the external environment. This is accomplished by first understanding the bark hydraulic architecture and its linkage to the environment, followed by its linkage to various tree processes. These linkages have not been thoroughly quantified, especially on an intra-annual (e.g. daily) scale. The study of bark hydraulic dynamics is of great interest because it is a relatively new topic with great potential. The changes of the bark in response to the environment may play a large part as a regulator to other tree processes. The thesis consists of four papers, of which one is a modelling paper and three are experimental (field and laboratory) studies. The model estimates growth by using dendrometer measurements as inputs for the model. Growth is estimated by separating the water-related influences from measured inner-bark, revealing a growth signal – proxy for cambial stem growth. Using this growth signal, a correlation study to microclimate variables is examined in one paper; and to assumed growth respiration in a second paper. The remaining two papers explore the seasonality of photosynthesis and respiration, and bark stem dynamics during the spring recovery period in the spring. As a conclusion of this thesis, these four papers show how inextricably linked, the individual tree processes are to the changes within the bark, due to the tight coupling with sap flow-related changes of the xylem. The culmination of this thesis opens new opportunities to further understand the dynamics of bark hydraulics and ecophysiological processes by implementing field measurements and state-of-the-art modelling.
Transmembrane Peptides as Sensors of the Membrane Physical State

Cell membranes are commonly considered fundamental structures having multiple roles such as confinement, storage of lipids, sustain and control of membrane proteins. In spite of their importance, many aspects remain unclear. The number of lipid types is orders of magnitude larger than the number of amino acids, and this compositional complexity is not clearly embedded in any membrane model. A diffused hypothesis is that the large lipid palette permits to recruit and organize specific proteins controlling the formation of specialized lipid domains and the lateral pressure profile of the bilayer. Unfortunately, a satisfactory knowledge of lipid abundance remains utopian because of the technical difficulties in isolating definite membrane regions. More importantly, a theoretical framework where to fit the lipidomic data is still missing. In this work, we wish to utilize the amino acid sequence and frequency of the membrane proteins as bioinformatics sensors of cell bilayers. The use of an alignment-free method to find a correlation between the sequences of transmembrane portion of membrane proteins with the membrane physical state suggested a new approach for the discovery of antimicrobial peptides.
Compensation of global movement for improved tracking of cells in time-lapse confocal microscopy image sequences

A bottleneck for high-throughput screening of live cells is the automated analysis of the generated image data. An important application in this context is the evaluation of the duration of cell cycle phases from confocal time-lapse microscopy image sequences, which typically involves a tracking step. The tracking step is an important part since it relates segmented cells from one time frame to the next. However, a main problem is that often the movement of single cells is superimposed with a global movement. The reason for the global movement lies in the high-throughput acquisition of the images and the repositioning of the microscope. If a tracking algorithm is applied to these images then only a superposition of the microscope movement and the cell movement is determined but not the real movement of the cells. In addition, since the displacements are generally larger, it is more difficult to determine the correspondences between cells. We have developed a phase-correlation based approach to compensate for the global movement of the microscope by registering each image of a sequence to a reference coordinate system. Our approach uses a windowing function in the spatial domain of the cross-power spectrum. This allows to determine the global movement by direct evaluation of the phase gradient, avoiding phase unwrapping. We present experimental results of applying our approach to synthetic and real image sequences. It turns out that the global movement can well be compensated and thus successfully decouples the global movement from the individual movement of the cells.
The Prevalence of Fibromyalgia in Patients with Restless Legs Syndrome

Amaç: Çalışmamızın amacı Huzursuz bacaklar sendromlu (HBS) hastalarda fibromiyalji (FM) sıklığını belirlemek, yaşam kalitesi ölçekleri ve FM arasındaki ilişkiyi değerlendirmektir. Gereç ve Yöntem: Çalışmamıza 18-65 yaş arasında HBS tanısı almış 30 hasta (20 kadın, 10 erkek) ve 30 sağlıklı kontrol (17 kadın, 13 erkek) katıldı. Hasta grubuna HBS Ağırlık Derecesi Ölçeği uygulanırken, hem hasta hem de kontrol grubuna Pittsburg Uyku Kalitesi İndeksi (PUKİ), Beck Depresyon Ölçeği, Beck Anksiyete Ölçeği ve Yaşam Kalitesi Kısa form-36 (KF-36) verildi. FM tanısı için Romatoloji Amerikan Koleji tarafından düzenlenen kriterler kullanıldı. Bulgular: Hastaların yaş ortalaması 44,73±11,23 yaş, kontrol grubun yaş ortalaması 46,00±12,23 yaş idi. Hastaların %36,7’sinde FM varken, kontrol grubunun %6,7’sinde vardı (p=0,01). Hastaların PUKİ, depresyon ve anksiyete skorları anlamlı olarak daha kötüydü (p=0,0001; p=0,004; p=0,000). Yaşam kalitesini değerlendirme ölçeğine (KF-36) göre ise HBS’si olanlarda enerji, ruhsal sağlık, sosyal fonksiyon, ağrı ve genel algı puanları anlamlı olarak daha yüksekken (p=0,004; p=0,023, p=0,0001; p=0,001; p=0,13), fiziksel ve emosyonel kısıtlılık puanları arasında kontrol grubu ile fark saptanmadı. Ancak HBS olanlarda ek olarak FM varlığı sadece vücut genel algı değerinde kötüleşmeye neden olmaktaydı (p=0,029). HBS ve FM bulguları olan hastalar hiçbir hastalığı olmayan grupla karşılaştırılınca en çok anksiyete puanlarında (üç kat) artma olduğu tespit edildi. Sonuç: Orta ve şiddetli HBS’li hastalarda FM sıktır (%36,67). HBS yaşam kalitesini bozmaktadır. Ancak iki hastalığın birlikteliği sadece hastaların kendi sağlıklarını değerlendirme skorlarını kötüleştirmekte ve en çok anksiyete skorlarını olumsuz etkilemektedir. Anahtar Kelimeler: Fibromiyalji, Huzursuz bacak sendromu, Kısa-form-36
Contents of Zn, Cu, Mn and Se in Milk in Relation to their Concentrations in Blood, Milk Yield and Stage of Lactation in Dairy Cattle

Pechova A. , L. Pavlata, R. Dvořak, E. Lokajova: Contents of Zn, Cu, Mn and Se in Milk in Relation to their Concentrations in Blood, Milk Yield and Stage of Lactation in Dairy Cattle. Acta Vet. Brno 2008, 77: 523-531. The objective of the study was to assess the effect of actual daily milk production and lactation stage on concentrations of Zn, Mn, Cu and Se in milk, and monitor correlations between milk and blood concentrations of these microelements. The study was performed in a herd of Holstein cattle with the average milk yield of 8,562 kg. Thirty-five dairy cows housed in one group were included in the study. Blood and milk samples were taken during two separate milk yield checks done 4 weeks apart. Actual milk production of monitored cows ranged from 19.6 to 62.6 l daily. For lactation stages we evaluated results of examinations performed from 7 to 188 days of lactation. Blood examinations showed that the cows included in our study had good supplementation with the microelements in question. Milk concentrations of individual microelements were as follows: 3855.2  814.7 μg/l of Zn; 36.3  14.4 μg/l of Cu; 20.1  8.3 μg/l of Mn, and 28.6  7.1 μg/l of Se. The effect of daily milk production on milk concentrations of the microelements was identified only for copper (r = -0.302, p  0.05). The variable of days of lactation (not considering days of the colostrum period) showed a positive correlation in manganese (r = 0.419, p  0.01); copper and selenium showed negative correlations (Cu: r = -0.258, p  0.05; Se: r = -0.277, p  0.05). The daily milk production influenced negatively only Cu concentration in milk, but Se, Zn and Mn was not influenced.With advancing lactation after colostrum period the concentration of Mn in milk raised, the concentration of Cu and Se declined and the concentration of Zn was
Efficient NUFFT-based direct Fourier algorithm for fan beam CT reconstruction

Related to the demand for fast and efficient tomographic reconstruction methods, the interest for Direct Fourier (DF) methods, which have a reduced computational complexity, has been growing. In this paper we present a new NUFFT-based DF reconstruction method which can be directly applied to fan-beam CT data sets avoiding the interpolation in Radon space as well as the interpolation in Fourier space. The performance of the new algorithm, in ideal and noisy conditions, is compared to those of other well known reconstruction methods, revealing an excellent behavior, specially in noisy conditions.
Environmental influence on the secondary productivity and fish abundance in coastal fishing grounds off Mangalore, south-eastern Arabian Sea

Environmental parameters influence the productivity and abundance of fish in marine ecosystems. In this study, we attempted to analyse the relationship between environmental parameters and abundance of fish in trawling grounds in south-eastern Arabian Sea along the coast of Karnataka. Among the 85 species of finfishes and shellfishes caught in the trawling grounds, 41 finfish species, 24 crustaceans, 18 molluscs and two echinoderms were recorded. Seasonal differences were seen in biomass with the highest biomass during the post-monsoon period (October-January). Water temperature and nutrients were the key contributing factors of seasonal differences in the biotic communities studied. Season specific diagnostic species were identified using SIMPER analysis. Squilla which formed the major prey item of most of the demersal fishes dominated (>40%) coastal grounds throughout all seasons. This could be considered as a fishery indicator of the region. The dominance and abundance of copepods was found to be influenced by sea surface temperature (SST) and nutrients. The results of the study have implications on the fishery, knowledge on environmental factors influencing the abundance and importance of non-commercial species in sustaining the fishery in the region.
Are Computer Science and Engineering Graduates Ready for the Software Industry? Experiences from an Industrial Student Training Program

It has been 50 years since the term "software engineering" was coined in 1968 at a NATO conference. The field should be relatively mature by now, with most established universities covering core software engineering topics in their Computer Science programs and others offering specialized degrees. However, still many practitioners lament a lack of skills in new software engineering hires. With the growing demand for software engineers from the industry, this apparent gap becomes more and more pronounced. One corporate strategy to address this gap is for the industry to develop supplementary training programs before the hiring process, which could also help companies screen viable candidates. In this paper, we report on our experiences and lessons learned in conducting a summer school program aimed at screening new graduates, introducing them to core skills relevant to the organization and industry, and assessing their attitudes toward mastering those skills before the hiring process begins. Our experience suggests that such initiatives can be mutually beneficial for new hires and companies alike. We support this insight with pre- and post-training data collected from the participants during the first edition of the summer school and a follow-up questionnaire conducted after a year with the participants, 50% of whom were hired by the company shortly after the summer school
The AIP 2 E 3 ligase acts as a novel negative regulator of ABA signaling by promoting ABI 3 degradation

The phytohormone abscisic acid (ABA) mediates many complex aspects of plant development including seed maturation, dormancy, and germination as well as root growth. The B3-domain transcription factor abscisic acid-insensitive 3 (ABI3) is a central regulator in ABA signaling, but little is known of how this factor is regulated. Here, we show that ABI3 is an unstable protein and that an ABI3-interacting protein (AIP2), which contains a RING motif, can polyubiquitinate ABI3 in vitro. The AIP2 E3 ligase activity is abolished by mutations (C230S; C231S) in the RING motif and the AIP2 (C/S) mutant functions in a dominant-negative manner. AIP2 has a stronger binding affinity for the B2 + B3 domain of ABI3 than the A1 + B1 domain, but only ubiquitinates the latter. In double-transgenic plants, induced AIP2 expression leads to a decrease in ABI3 protein levels. In contrast, ABI3 levels are elevated upon induced expression of the AIP2 RING mutant, which interferes with the endogenous AIP2 E3 activity. An aip2-1-null mutant shows higher ABI3 protein levels compared with wild type after seed stratification, and is hypersensitive to ABA, mimicking the ABI3-overexpression phenotype, whereas AIP2-overexpression plants contain lower levels of ABI3 protein than wild type and are more resistant to ABA, phenocopying abi3. Our results indicate that AIP2 negatively regulates ABA signaling by targeting ABI3 for post-translational destruction.
Ontology and the Lexicon: Formal ontology as interlingua: the SUMO and WordNet linking project and global WordNet

WordNet1 is a large lexical database for English. With its broad coverage and a design that is useful for a range of natural-language processing applications, this resource has found wide general acceptance. We offer only a brief description here and refer the reader to Miller, 1990 and Fellbaum, 1998 for further details. WordNet’s creation in the mid-1980s was motivated by current theories of human semantic organization (Collins and Quillian, 1969). People have knowledge about tens of thousands of concepts, and the words expressing these concepts must be stored and retrieved in an efficient and economic fashion. A semantic network such as WordNet is an attempt to model one way in which concepts and words could be organized. The basic unit of WordNet is a set of cognitively equivalent synonyms, or synset. Examples of a noun, verb, and adjective synset are { vacation, holiday }, { close, shut }, and { soiled, dirty }, respectively. Each synset represents a concept, and each member of a synset encodes the same concept. Differently put, synset members are interchangeable in many contexts without changing the truth value of the context. Each synset also includes a definition, or ‘gloss’, and an illustrative sentence. The current version of WordNet (3.0) contains over 117,000 synsets that are organized into a huge semantic network. The synsets are interlinked by means of bidirectional semantic relations such as hyponymy, meronymy, and a number of entailment relations. For example, the relation between oak and tree is such that oak is encoded as a hyponym (subordinate) of tree and tree is encoded as a hypernym (superordinate) of oak. Leaf and trunk are meronyms (parts) of tree, their holonym. Meronyms are transitive, so linking leaf and trunk to tree means that oak (and beech and maple etc.) inherits leaf and trunk as parts by virtue of its relation to tree (Miller, 1990, 1998). Concepts expressed by other parts of speech (verbs, adjectives) are interlinked by means of additional relations (Fellbaum, 1998).
Genetic admixture between the Iberian endemic lizards Podarcis bocagei and Podarcis carbonelli : evidence for limited natural hybridization and a bimodal hybrid zone

When recently diverged taxa come into contact, the extent of introgression between them is related to the degree of differentiation that they have achieved. Studying contact zones is therefore essential to understand if differentiated taxa are reproductively isolated and, ultimately, if they are likely to remain distinct. Recent work on Iberian and North African wall lizards (Podarcis) has documented the existence of multiple evolutionary units, diagnosable both by genetic markers and morphology, but suggests that gene flow between distinct forms has occurred. Therefore, we were interested in evaluating how species boundaries are maintained in the areas where they meet. In this work, we study the contact zone between Podarcis bocagei and Podarcis carbonelli. We sampled a transect including the only locality where these two lizards are known to occur in syntopy and analysed a battery of 15 unlinked nuclear genetic markers and mitochondrial DNA. We also conducted a preliminary analysis of morphology and fertility. Using model-based clustering approaches, we show that the two species hybridize in the population where they have direct contact, but evidences of introgression are low for nearby populations. Although a significant number of individuals show evidence of admixture, this hybrid zone is clearly bimodal, suggesting strong barriers to gene flow, of which the putative nature are discussed. Interestingly, morphological analyses do not support the existence of intermediate forms among individuals that are admixed genetically. Taken together, these results constitute further evidence validating P. bocagei and P. carbonelli as distinct species.
Title : Assessing strengths and weaknesses of DNA metabarcoding based 1 macroinvertebrate identification for routine stream monitoring

3 Running Title (45 char max): Stream bioassessment using DNA metabarcoding 4 Word count: 7766 5 Authors: Vasco Elbrecht, Ecaterina Edith Vamos, Kristian Meissner, Jukka Aroviita, Florian Leese 6 7 Affiliations: 8 1) Aquatic Ecosystem Research, Faculty of Biology, University of Duisburg-Essen, Universitätsstraße 5, 45141 Essen, 9 Germany 10 2) Finnish Environment Institute, Freshwater Centre, Survontie 9 A, 40500 Jyväskylä, Finland 11 3) Finnish Environment Institute, Freshwater Centre, PO Box 413, 90014 Oulu, Finland 12 4) Centre for Water and Environmental Research (ZWU) Essen, University of Duisburg-Essen, Universitätsstraße 2, 45141 13 Essen, Germany 14 15 *Corresponding author: florian.leese@uni-due.de, phone: +49.201-1834053 16 17
Depression And Anger As Risk Factors For Suicide With Inpatient Adolescents

Suicide is the third leading cause of death for children ages 10-24 (U.S. Department of Health and Human Services, Centers for Disease Control and Prevention, 2010). This study examined the direct and indirect effects of depression, anger, and coping with regard to adolescent suicidal behavior. Seventy six participants from an inpatient psychiatric hospital were evaluated for depression, state and trait anger, and coping skills using the Children’s Depression Inventory, State-Trait Anger Expression Inventory, and the Coping Response Inventory. The results showed there were statistically significant direct effects of depression and state and trait anger with adolescents who made a suicide attempt compared to those with suicide ideation and no attempt. The results of the Children’s Depression Inventory scores indicated that a cutoff score of 68 or higher is a good predictor of an increased risk of suicide. The adolescents at highest risk for suicide were significantly depressed, had elevated state and trait anger, displayed high emotional discharge, and could not identify a solution to their problems.
Is Metformin a Safe and Effective Treatment of Gestational Diabetes Mellitus

Maternal and perinatal complications related to maternal hyperglycemia are Cesarean Section (CS), pregnancy induced hypertension, excessive fetal growth, leading to large for gestational age infants or macrosomia and a subsequent higher risk of shoulder dystocia, birth injuries and stillbirth [4-6]. An adequate glycaemic control is necessary to reduce the incidence of these adverse pregnancy outcomes [2]. The glycaemic targets were traditionally achieved by insulin therapy, which had been considered the standard practice for women with GDM who could not have been controlled by diet and physical activity. However, this treatment, due to requirement of multiple daily injections and the risk of hypoglycaemia, could be difficult to manage for