Miracle-dz/UniFAR-FTUs huggingface dataset:
Robust object tracking with depth data

Object tracking plays a vital role in the future of Robotics as it is used for motion planning and decision making. In recent years, research in object tracking has focussed on designing tracking methods that do not rely on a pre-learned model of the object and are therefor able to track any kind of object. As a result, online learning of an object model is used in virtually all new methods. However, these tracking methods often fail when presented with articulated objects or when an object rotates enough that parts become visible that haven’t been seen before. Furthermore, these methods rely purely on texture and have no notion of object shape. Additionaly, almost no existing tracking method processes images fast enough to be practically applied in Robotics applications. Affordable depth sensors have started to become popular. These sensors work as normal cameras, but with an additional depth channel. This depth information contains information about the shape of objects, which can be used to recognize the difference between object and background, or to learn a more accurate model of the object of interest. In this work, novel methods are introduced to improve tracker accuracy. Acknowledging that introducing novel methods, tracking speeds are likely to decrease, two additional methods of increasing the tracker speed are proposed. K-means clustering and local searching are applied to increase tracker speed, while depth information is used in two ways to improve accuracy. Gaussian Mixture Modelling of the depth histogram is applied to segment object from background and shape features based on local curvature are used in a Random Forests classification method to learn an object model that includes shape information.
Benchmark problems for dynamic modeling of intracellular processes

Motivation Dynamic models are used in systems biology to study and understand cellular processes like gene regulation or signal transduction. Frequently, ordinary differential equation (ODE) models are used to model the time and dose dependency of the abundances of molecular compounds as well as interactions and translocations. A multitude of computational approaches have been developed within recent years. However, many of these approaches lack proper testing in application settings because a comprehensive set of benchmark problems is yet missing. Results We present a collection of 20 ODE models developed given experimental data as benchmark problems in order to evaluate new and existing methodologies, e.g. for parameter estimation or uncertainty analysis. In addition to the equations of the dynamical system, the benchmark collection provides experimental measurements as well as observation functions and assumptions about measurement noise distributions and parameters. The presented benchmark models comprise problems of different size, complexity and numerical demands. Important characteristics of the models and methodological requirements are summarized, estimated parameters are provided, and some example studies were performed for illustrating the capabilities of the presented benchmark collection. Availability The models are provided in several standardized formats, including an easy-to-use human readable form and machine-readable SBML files. The data is provided as Excel sheets. All files are available at https://github.com/Benchmarking-Initiative/Benchmark-Models, with MATLAB code to process and simulate the models. Contact jan.hasenauer@helmholtz-muenchen.de, ckreutz@fdm.uni-freiburg.de
Neural induction of porcine‐induced pluripotent stem cells and further differentiation using glioblastoma‐cultured medium

Prior to transplantation, preclinical study of safety and efficacy of neural progenitor cells (NPCs) is needed. Therefore, it is important to generate an efficient in vitro platform for neural cell differentiation in large animal models such as pigs. In this study, porcine‐induced pluripotent stem cells (iPSCs) were seeded at high cell density to a neural induction medium containing the dual Sma‐ and Mad‐related protein (SMAD) inhibitors, a TGF‐β inhibitor and BMP4 inhibitor. The dSMADi‐derived NPCs showed NPC markers such as PLAG1, NESTIN and VIMENTIN and higher mRNA expression of Sox1 compared to the control. The mRNA expression of HOXB4 was found to significantly increase in the retinoic acid‐treated group. NPCs propagated in vitro and generated neurospheres that are capable of further differentiation in neurons and glial cells. Gliobalstoma‐cultured medium including injury‐related cytokines treated porcine iPSC‐NPCs survive well in vitro and showed more neuronal marker expression compared to standard control medium. Collectively, the present study developed an efficient method for production of neural commitment of porcine iPSCs into NPCs.
Physical Therapy Intervention for Women With Dyspareunia: A Randomized Clinical Trial

Abstract Dyspareunia negatively affects women´s quality of life, and is a frequent complaint during the peri- and postmenopausal period. A randomized trial evaluated sexual function, quality of life, pain, and pelvic floor muscle function of climacteric women aged between 40 and 60 years old who were sexually active and had complaints of dyspareunia for at least six months. They were assessed before and after their randomization in one of the following interventions: the first group (n = 21) received five one-hour sessions of thermotherapy for relaxation of pelvic floor muscles, myofascial release, and pelvic training (pelvic floor muscle training—PFMT group). The second group (n = 21) received five one-hour sessions during which heat was applied to the lower back with myofascial release of abdominal diaphragm, piriformis, and iliopsoas muscles, with no involvement of pelvic training (lower back—LB group). Forty-two climacteric women with dyspareunia (mean ± SD, PFMT group: 51.9 ± 5.3 years, LB group: 50.6 ± 4.7 years, Student’s t-test, p = 0.397) were studied. Pain scores (mean ± SEM) in the PFMT group decreased from 7.77 ± 0.38 to 2.25 ± 0.30; and in the LB group from 7.62 ± 0.29 to 5.58 ± 0.49 (generalized estimating equation—GEE model, p ≤ 0.001 for group, time, and interaction pairwise comparisons). Conclusion: The proposed pelvic floor muscle training protocol was effective to improve pain, quality of life, sexual function, and pelvic floor muscle function in climacteric women with dyspareunia.
Dietary Fatty Acids Amplify Inflammatory Responses to Infection through p38 MAPK Signaling

&NA; Obesity is an important risk factor for severe asthma exacerbations, which are mainly caused by respiratory infections. Dietary fatty acids, which are increased systemically in obese patients and are further increased after high‐fat meals, affect the innate immune system and may contribute to dysfunctional immune responses to respiratory infection. In this study we investigated the effects of dietary fatty acids on immune responses to respiratory infection in pulmonary fibroblasts and a bronchial epithelial cell line (BEAS‐2B). Cells were challenged with BSA‐conjugated fatty acids (&ohgr;‐6 polyunsaturated fatty acids [PUFAs], &ohgr;‐3 PUFAs, or saturated fatty acids [SFAs]) +/‐ the viral mimic polyinosinic:polycytidylic acid (poly[I:C]) or bacterial compound lipoteichoic acid (LTA), and release of proinflammatory cytokines was measured. In both cell types, challenge with arachidonic acid (AA) (&ohgr;‐6 PUFA) and poly(I:C) or LTA led to substantially greater IL‐6 and CXCL8 release than either challenge alone, demonstrating synergy. In epithelial cells, palmitic acid (SFA) combined with poly(I:C) also led to greater IL‐6 release. The underlying signaling pathways of AA and poly(I:C)‐ or LTA‐induced cytokine release were examined using specific signaling inhibitors and IB. Cytokine production in pulmonary fibroblasts was prostaglandin dependent, and synergistic upregulation occurred via p38 mitogen‐activated protein kinase signaling, whereas cytokine production in bronchial epithelial cell lines was mainly mediated through JNK and p38 mitogen‐activated protein kinase signaling. We confirmed these findings using rhinovirus infection, demonstrating that AA enhances rhinovirus‐induced cytokine release. This study suggests that during respiratory infection, increased levels of dietary &ohgr;‐6 PUFAs and SFAs may lead to more severe airway inflammation and may contribute to and/or increase the severity of asthma exacerbations.
Assessment and Treatment of the Anorexia of Aging: A Systematic Review

(1) Background: Appetite loss in older people, the ‘Anorexia of Aging’ (AA), is common, associated with under-nutrition, sarcopenia, and frailty and yet receives little attention. This review had two aims: describe interventions for AA and their effectiveness, and identify the methods of appetite assessment. (2) Methods: Study inclusion: participants aged ≥65, intervention for AA, and appetite assessment, any design, and comparator. Exclusion: studies on specific health cohorts. Searches in four databases with hand searching of references and citing works. Two researchers independently assessed eligibility and quality. (3) Results: Authors screened 8729 titles, 46 full texts. Eighteen articles were included describing nine intervention types: education (n = 1), exercise (n = 1), flavor enhancement (n = 2), increased meal variety (n = 1), mealtime assistance (n = 1), fortified food (n = 1), oral nutritional supplement (ONS) (n = 8), amino acids (n = 1), and medication (n = 2). Three studies evaluated combinations: education + exercise, ONS + exercise, and ONS + medication. Five intervention types exhibited favorable effects on appetite but in single datasets or not replicated. Appetite was assessed predominantly by Likert (n = 9), or visual analogue scales (n = 7). (4) Conclusions: A variety of interventions and methods of appetite assessments were used. There was a lack of clarity about whether AA or undernutrition was the intervention target. AA is important for future research but needs standardized assessment so that effectiveness of a range of interventions can be fully explored.
Micro-Electrode-Dot-Array Digital Microfluidic Biochips: Technology, Design Automation, and Test Techniques

Digital microfluidic biochips (DMFBs) are being increasingly used for DNA sequencing, point-of-care clinical diagnostics, and immunoassays. DMFBs based on a micro-electrode-dot-array (MEDA) architecture have recently been proposed, and fundamental droplet manipulations, e.g., droplet mixing and splitting, have also been experimentally demonstrated on MEDA biochips. There can be thousands of microelectrodes on a single MEDA biochip, and the fine-grained control of nanoliter volumes of biochemical samples and reagents is also enabled by this technology. MEDA biochips offer the benefits of real-time sensitivity, lower cost, easy system integration with CMOS modules, and full automation. This review paper first describes recent design tools for high-level synthesis and optimization of map bioassay protocols on a MEDA biochip. It then presents recent advances in scheduling of fluidic operations, placement of fluidic modules, droplet-size-aware routing, adaptive error recovery, sample preparation, and various testing techniques. With the help of these tools, biochip users can concentrate on the development of nanoscale bioassays, leaving details of chip optimization and implementation to software tools.
Reconciling the opposing effects of neurobiological evidence on criminal sentencing judgments

Legal theorists have characterized physical evidence of brain dysfunction as a double-edged sword, wherein the very quality that reduces the defendant’s responsibility for his transgression could simultaneously increase motivations to punish him by virtue of his apparently increased dangerousness. However, empirical evidence of this pattern has been elusive, perhaps owing to a heavy reliance on singular measures that fail to distinguish between plural, often competing internal motivations for punishment. The present study employed a test of the theorized double-edge pattern using a novel approach designed to separate such motivations. We asked a large sample of participants (N = 330) to render criminal sentencing judgments under varying conditions of the defendant’s mental health status (Healthy, Neurobiological Disorder, Psychological Disorder) and the disorder’s treatability (Treatable, Untreatable). As predicted, neurobiological evidence simultaneously elicited shorter prison sentences (i.e., mitigating) and longer terms of involuntary hospitalization (i.e., aggravating) than equivalent psychological evidence. However, these effects were not well explained by motivations to restore treatable defendants to health or to protect society from dangerous persons but instead by deontological motivations pertaining to the defendant’s level of deservingness and possible obligation to provide medical care. This is the first study of its kind to quantitatively demonstrate the paradoxical effect of neuroscientific trial evidence and raises implications for how such evidence is presented and evaluated.
Ocular Findings in Yellow Fever Infection

Importance Yellow fever virus (YFV) is a reemerging, potentially lethal arboviral disease that has been occurring recently in Africa and South America. Poor levels of immunization have facilitated the viral spread in southeastern Brazil, leading to an unprecedented outbreak that started in late 2016. Although human cases have been linked to sylvatic mosquitoes, the concern is that YFV may spread to urban centers infested with Aedes aegypti and Aedes albopictus mosquitoes and start a true urban cycle. Objective To describe the ocular findings in patients with acute YFV infection. Design, Setting, Participants Two adults with an acute YFV infection in southeastern Brazil underwent an ophthalmologic and ocular ultrasonographic examination in early 2018. Main Outcomes and Measures Ocular findings in patients with acute YFV infection. Results Both patients presented with increased choroidal thickness bilaterally seen on ocular ultrasonography. A man in his late 50s who had not been vaccinated previously also presented with bilateral, midperipheral, 360° choroidal detachment and yellowish subretinal lesions. After clinical deterioration and liver transplant, the man died. A woman in her early 30s who had been vaccinated previously for YFV presented with increased retinal venous congestion bilaterally. She was discharged with mild conjunctival chemosis and icterus. Conclusions and Relevance These reports describe different patterns of ocular findings associated with YFV acute infection. However, the exact mechanism involved in the retinal and choroidal findings remains unclear.
RNase H1 promotes replication fork progression through oppositely transcribed regions of Drosophila mitochondrial DNA

Mitochondrial DNA (mtDNA) replication uses a simple core machinery similar to those of bacterial viruses and plasmids, but its components are challenging to unravel. Here, we found that, as in mammals, the single Drosophila gene for RNase H1 (rnh1) has alternative translational start sites, resulting in two polypeptides, targeted to either mitochondria or the nucleus. RNAi-mediated rnh1 knockdown did not influence growth or viability of S2 cells, but compromised mtDNA integrity and copy number. rnh1 knockdown in intact flies also produced a phenotype of impaired mitochondrial function, characterized by respiratory chain deficiency, locomotor dysfunction, and decreased lifespan. Its overexpression in S2 cells resulted in cell lethality after 5–9 days, attributable to the nuclearly localized isoform. rnh1 knockdown and overexpression produced opposite effects on mtDNA replication intermediates. The most pronounced effects were seen in genome regions beyond the major replication pauses where the replication fork needs to progress through a gene cluster that is transcribed in the opposite direction. RNase H1 deficiency led to an accumulation of replication intermediates in these zones, abundant mtDNA molecules joined by four-way junctions, and species consistent with fork regression from the origin. These findings indicate replication stalling due to the presence of unprocessed RNA/DNA heteroduplexes, potentially leading to the degradation of collapsed forks or to replication restart by a mechanism involving strand invasion. Both mitochondrial RNA and DNA syntheses were affected by rnh1 knockdown, suggesting that RNase H1 also plays a role in integrating or coregulating these processes in Drosophila mitochondria.
Risk Factors for Peer Victimization among Middle and High School Students

Peer victimization at school is a pressing public health issue. Peer victimization has a deleterious impact on the victim and can lead to lifelong negative outcomes such as depression. The purpose of the present study is to examine peer victimization and potential individual, school, and peer correlates in a national sample of middle and high school students. A secondary data analysis of the School Crime and Safety survey was conducted to investigate study aims. Greater than one in 20 (7.2%) of students reported peer victimization at school. Multiple individual factors were found to increase the odds of victimization including grade level, grades received, and school avoidance among other variables. School and peer factors were also found to be significant. Study findings may be useful to school personnel for reducing peer victimization at school. Specific recommendations for school personnel are offered.
Influence of microphone soiling on syllable recognition in cochlear implants: simulation and recognition in noise

Abstract Background: The microphone is the first link of the sound processing chain and if there is dirt on the membrane or in the input port, the frequency response is modified. Objective: The effect of microphone cleaning in cochlear implants (CI) was studied by measuring speech perception scores in the noise of CI users and of normal hearing (NH) subjects with a CI simulator. Material and methods: Sixty-one adult CI users and 20 NH were tested. In CI subjects, speech comprehension scores in noise were compared before and after cleaning microphone ports with one of two different cleaning procedures. NH listeners were tested using a vocoder that simulated soiled microphones. Two main coding schemes were considered, channel-picking (CP) and fixed-channel (FC). Results: With NH subjects, the effect of the coding strategy and degree of soiling was statistically significant (p < 10−4); for the intermediate signal to noise ratios (SNRs), the recognition percentages were clearly affected. With CI users, cleaning the microphones significantly improved the recognition scores (p < 10−4). The two cleaning procedures considered turned out to be significantly different (p < 10−4). Conclusions: It is suggested to perform a regular microphone port cleaning to avoid deep soiling which leads to a decrease in speech understanding.
Novel SNARE Complex Polymorphisms Associated with Multiple Sclerosis: Signs of Synaptopathy in Multiple Sclerosis

Background It is well known that axonal degeneration plays a role in disability in patients with multiple sclerosis, and synaptopathy has recently become an important issue. Aims To investigate the possible roles of selected synaptic and presynaptic membrane protein genetic polymorphisms (VAMP2, SNAP-25, synaptotagmin, and syntaxin 1A) in patients with multiple sclerosis. Study Design Case-control study. Methods A total of 123 patients with multiple sclerosis and 192 healthy controls were included. The functional polymorphisms of specific SNARE complex proteins (VAMP2, synaptotagmin XI, syntaxin 1A, and SNAP-25) were analyzed by polymerase chain reaction. Results Significant differences were detected in the genotype and allele distribution of 26-bp Ins/Del polymorphisms of VAMP2 between patients with multiple sclerosis and control subjects; Del/Del genotype and Del allele of VAMP2 were more frequent in patients with multiple sclerosis (p=0.011 and p=0.004, respectively). Similarly, Ddel polymorphism of SNAP-25 gene C/C genotype (p=0.059), syntaxin 1A T/C and C/C genotypes (p=0.005), and synaptotagmin XI gene C allele (p=0.001) were observed more frequently in patients with multiple sclerosis. CC, syntaxin rs1569061 1A gene for 33-bp promoter region TC haplotypes, and synaptotagmin XI gene were found to be associated with an increased risk for multiple sclerosis (p=0.012). Similarly, GC haplotype for rs3746544 of SNAP-25 gene and rs1051312 of SNAP-25 gene were associated with an increased risk for multiple sclerosis (p=0.022). Conclusion Genetic polymorphisms of SNARE complex proteins, which have critical roles in synaptic structure and communication, may play a role in the development of multiple sclerosis.
Patients with SATB2‐associated syndrome exhibiting multiple odontomas

Special AT‐rich sequence‐binding protein 2 (SATB2)‐associated syndrome (SAS) is characterized by alterations of SATB2. Its clinical features include intellectual disability and craniofacial abnormalities, such as cleft palate, dysmorphic features, and dental abnormalities. Here, we describe three previously undiagnosed, unrelated patients with SAS who exhibited dental abnormalities, including multiple odontomas. Although isolated odontomas are common, multiple odontomas are rare. Individuals in families 1 and 3 underwent whole‐exome sequencing. Patient 2 and parents underwent targeted amplicon sequencing. On the basis of the hg19/GRCh37 reference and the RefSeq mRNA NM_001172517, respective heterozygous mutations were found and validated in Patients 1, 2, and 3: a splice‐site mutation (chr2:g.200137396C > T, c.1741‐1G > A), a nonsense mutation (chr2:g.200213750G > A, c.847C > T, p.R283*), and a frame‐shift mutations (chr2:g.200188589_200188590del, c.1478_1479del, p.Q493Rfs*19). All mutations occurred de novo. The mutations in Patients 1 and 3 were novel; the mutation in Patient 2 has been described previously. Tooth mesenchymal cells derived from Patient 2 showed diminished SATB2 expression. Multiple odontomas were evident in the patients in this report; however, this has not been recognized previously as a SAS‐associated phenotype. We propose that multiple odontomas be considered as an occasional manifestation of SAS.
Compatibility of 3D printing materials and printing techniques with PAGAT gel dosimetry

Polymer gel (PG) dosimetry enables three dimensional (3D) measurement of complex dose distributions. However, PGs are strongly reactive with oxygen and other contaminations, limiting their applicability by the need to use specific container materials. We investigate different 3D printing materials and printing techniques for their compatibility with PG. Suitable 3D printing materials may provide the possibility to perform PG dosimetry in complex-shaped phantoms. 3D printed and PG-filled test vials were irradiated homogenously. The signal response was evaluated with respect to homogeneity and compared to the signal in already validated reference vials. In addition, for the printing material VeroClear™ (StrataSys, Eden Prairie, USA) different methods to remove support material, which was required during the printing process, were investigated. We found that the support material should be used only on the outer side of the container wall with no direct contact to the PG. With the VeroClear™ material a homogenous signal response was achieved with a mean deviation of relative to the reference vials. In addition, the homogeneous irradiation of an irregularly-shaped gel container designed with the same printing material and technique also lead to a homogenous PG response. Furthermore, a small field irradiation of an additional test-vial showed an accurate representation of steep dose gradients with a deviation of the maximum position of relative to the reference vial.