Miracle-dz/UniFAR-FTUs huggingface dataset:
A 2.4GHz Non-Contact Biosensor System for Continuous Monitoring of Vital-Signs

In this chapter, we present a novel Doppler-based vital signs biosensor that can monitor the respiration and heartbeat rates of a person remotely without the need of any obstructions like patches, cords, etc. We will discuss the sensor operation principle and present three generations of systems that were designed to accurately extract the respiration rate and heartbeat of subjects using the Doppler radar principle. The systems have been realized using discrete custom off the shelf (COTS) parts. The first generation of the biosensor system consisted of discrete RF components system and a bulky SRS560 amplifier and filter box. Later generations of sensors consisted of custom designed printed circuits boards (PCBs) for the Doppler transceiver and for performing the analog signal processing. The data obtained using these non-contact biosensor systems was processed and logged in real-time using a LabVIEW© Graphic User Interface (GUI). Digital signal processing extracts the vital signs by filtering, auto correlating and calculating the Discrete Fourier Transform (DFT) of the waveforms. A comparison of performance among the three different generations of sensors shows that a quadrature transceiver system using autocorrelation can extract the respiration rates and heartbeat rates most accurately. Our single PCB version of the biosensor system was found to perform as well as the system using bulky components and SRS560 box. Good data accuracy has been observed on the quadrature radar sensor system with mean detection errors for respiration rate within ~1 beat/min and for heart rate within ~3 beat/min. The continuous vital signs data measured from these portable sensors can also be wirelessly transferred to healthcare professionals to make life saving decisions and diagnosis of symptoms. In the future, our vision is that a continuous log of these vital signs info can also be used to remotely monitor and gauge the recovery of patients, and even for the prevention or prediction of severe illnesses and complications.
Hemodynamic Changes After Administration of Mannitol Measured by a Noninvasive Cardiac Output Monitor

Mannitol is the most commonly used hyperosmotic agent in neurosurgery. Being an agent that increases intravascular volume by withdrawing water from the brain, it may cause significant changes in stroke volume (SV), cardiac output (CO), systemic vascular resistance and blood pressure. In this study, we monitored the hemodynamic changes in response to a single dose of mannitol by using a noninvasive CO monitorbased on the thoracic electrical bioimpedance technique, in patients undergoing craniotomy. Eleven adult patients undergoing elective craniotomy received mannitol 1.0 g/kg 15 minutes before dural opening. The following hemodynamic variables were recorded: heart rate, systolic blood pressure, diastolic blood pressure, SV, CO, and cardiac index. The measurements were made before the administration of mannitol, at 1, 2, 5, 10, 15, 20, 25, 30, 35, 40, and 45 minutes after the termination of the mannitol infusion. Urine output was measured at 10, 20, 30, 40, 50, 60, 90, and 120 minutes after termination of the mannitol infusion. Heart rate values from 25 to 45 minutes were significantly lower compared with the premannitol values (P<0.05). All the postmannitol systolic blood pressure values were significantly lower than the premannitol value (P<0.05). SV increased significantly for 15 minutes after administration of mannitol (P<0.05). SV at 45 minutes was significantly lower than that from 1 to 30 minutes (P<0.05). Cardiac index also showed a similar change with a significant increase at 1 to 10 minutes and a decrease at 40 to 45 minutes compared with 1 to 15 minutes.The rate of urine secretion was higher during the first 10 minutes (40±15 mL/kg/ h) than during the rest of the study period. The overall fluid balance at the end of 120 minutes was −370±987 mL. In this study using noninvasive measurement of CO by thoracic bioimpedance plethysmography during craniotomy, a single bolus dose of mannitol 1.0 g/kg caused a significant but short duration changes in the hemodynamic variables. The changes in SV, and CO, lasted for only 15 minutes after the infusion.
Automatically Identifying Implicit Arguments to Improve Argument Linking and Coherence Modeling

Implicit arguments are a discourse-level phenomenon that has not been extensively studied in semantic processing. One reason for this lies in the scarce amount of annotated data sets available. We argue that more data of this kind would be helpful to improve existing approaches to linking implicit arguments in discourse and to enable more in-depth studies of the phenomenon itself. In this paper, we present a range of studies that empirically validate this claim. Our contributions are threefold: we present a heuristic approach to automatically identify implicit arguments and their antecedents by exploiting comparable texts; we show how the induced data can be used as training data for improving existing argument linking models; finally, we present a novel approach to modeling local coherence that extends previous approaches by taking into account non-explicit entity references.
Synthetic Fragments of Vibrio cholerae O1 Inaba O-Specific Polysaccharide Bound to a Protein Carrier Are Immunogenic in Mice but Do Not Induce Protective Antibodies

ABSTRACT Development of Vibrio cholerae lipopolysaccharide (LPS) as a cholera vaccine immunogen is justified by the correlation of vibriocidal anti-LPS response with immunity. Two V. cholerae O1 LPS serotypes, Inaba and Ogawa, are associated with endemic and pandemic cholera. Both serotypes induce protective antibody following infection or vaccination. Structurally, the LPSs that define the serotypes are identical except for the terminal perosamine moiety, which has a methoxyl group at position 2 in Ogawa but a hydroxyl group in Inaba. The terminal sugar of the Ogawa LPS is a protective B-cell epitope. We chemically synthesized the terminal hexasaccharides of V. cholerae serotype Ogawa, which comprises in part the O-specific polysaccharide component of the native LPS, and coupled the oligosaccharide at different molar ratios to bovine serum albumin (BSA). Our initial studies with Ogawa immunogens showed that the conjugates induced protective antibody. We hypothesized that antibodies specific for the terminal sugar of Inaba LPS would also be protective. Neoglycoconjugates were prepared from synthetic Inaba oligosaccharides (disaccharide, tetrasaccharide, and hexasaccharide) and BSA at different levels of substitution. BALB/c mice responded to the Inaba carbohydrate (CHO)-BSA conjugates with levels of serum antibodies of comparable magnitude to those of mice immunized with Ogawa CHO-BSA conjugates, but the Inaba-specific antibodies (immunoglobulin M [IgM] and IgG1) were neither vibriocidal nor protective in the infant mouse cholera model. We hypothesize that the anti-Inaba antibodies induced by the Inaba CHO-BSA conjugates have enough affinity to be screened via enzyme-linked immunosorbent assay but not enough to be protective in vivo.
Integration Between the Epibranchial Placodes and the Hindbrain

Developmental integration results from coordination among components of different embryonic fields to realize the later anatomical and functional relationships. We demonstrate that in the chick head, integration between the epibranchial placodes and the hindbrain is achieved as the neuroglial hindbrain crest cells guide the epibranchial neuronal cells inward to establish their central connections. This work defines a role for the neuroglial hindbrain crest in organizing the afferent innervation of the hindbrain.
Caring for Vincent: A Chatbot for Self-Compassion

The digitization of mental health care holds promises of affordable and ubiquitously available treatment, e.g., with conversational agents (chatbots). While technology can guide people to care for themselves, we examined how people can care for another being as a way to care for themselves. We created a self-compassion chatbot (Vincent) and compared between caregiving and care-receiving conditions. Care-giving Vincent asked participants to partake in self-compassion exercises. Care-receiving Vincent shared its foibles, e.g., embarrassingly arriving late at an IP address, and sought out advice. While self-compassion increased for both conditions, only those with care-receiving Vincent significantly improved. In tandem, we offer qualitative data on how participants interacted with Vincent. Our exploratory research shows that when a person cares for a chatbot, the person's self-compassion can be enhanced. We further reflect on design implications for strengthening mental health with chatbots.
VRsneaky: Increasing Presence in VR Through Gait-Aware Auditory Feedback

While Virtual Reality continues to increase in fidelity, it remains an open question how to effectively reflect the user's movements and provide congruent feedback in virtual environments. We present VRsneaky, a system for producing auditory movement feedback, which helps participants orient themselves in a virtual environment by providing footstep sounds. The system reacts to the user's specific gait features and adjusts the audio accordingly. In a user study with 28 participants, we found that VRsneaky increases users' sense of presence as well as awareness of their own posture and gait. Additionally, we find that increasing auditory realism significantly influences certain characteristics of participants' gait. Our work shows that gait-aware audio feedback is a means to increase presence in virtual environments. We discuss opportunities and design requirements for future scenarios where users walk through immersive virtual worlds.
Effect of Different Interferonα2 Preparations on IP10 and ET-1 Release from Human Lung Cells

Background Alfa-interferons (IFNα2a, IFNα2b, 40KDa-PEGIFNα2a and 12KDa-PEGIFNα2b) are effective treatments for chronic hepatitis C infection. However, their usage has been associated with a variety of adverse events, including interstitial pneumonitis and pulmonary arterial hypertension. Although rare, these adverse events can be severe and potentially life-threatening, emphasizing the need for simple biomarkers of IFN-induced lung toxicity. Methods Human lung microvascular endothelial cells (HLMVEC), human pulmonary artery smooth muscle (HPASM) cells and A549 cells were grown under standard conditions and plated into 96- or 6-well plates. Cells were stimulated with various concentrations of different IFNs in hydrocortisone-free medium. After 24 and 48 hours, IP10 and ET-1 were measured by ELISA in conditioned medium. In a second set of experiments, cells were pre-treated with tumour necrosis factor-α (TNF-α) (10 ng/mL). Results IFNα2a, IFNα2b, 40KDa-PEGIFNα2a and 12KDa-PEGIFNα2b, but not IFNλ, induced IP10 (CXCL10) release and increased IP10 gene induction in HLMVEC. In addition, all four IFNα preparations induced IP10 release from HPASM cells and A549 cells pre-treated with TNFα. In each of these cell types, 40KDa-PEGIFNα2a was significantly less active than the native forms of IFNα2a, IFNα2b or 12KDa-PEGIFNα2b. Similarly, IFNα2a, IFNα2b and 12KDa-PEGIFNα2b, but not 40KDa-PEGIFNα2a, induced endothelin (ET)-1 release from HPASM cells. Conclusions Consistent with other interstitial pulmonary diseases, both IP10 and ET1 may serve as markers to monitor IFN-induced lung toxicity in patients. In addition, both markers may also serve to help characterize the risk associated with IFNα preparations to induce lung toxicity.
Developmental Peculiarities and Seed-Borne Endophytes in Quinoa: Omnipresent, Robust Bacilli Contribute to Plant Fitness

Among potential climate change-adapted crops for future agriculture, quinoa (Chenopodium quinoa), a facultative halophyte plant with exceptional nutritional properties, stands out as a prime candidate. This work examined how quinoa deals with extreme situations during seed rehydration. Quinoa distinguishes itself from other plants in multiple ways. It germinates within minutes, even under extremely hostile conditions. Broken seeds/split embryos are able to regenerate. Furthermore, quinoa seedlings are resurrection-competent. These peculiarities became in part explainable upon discovery of seed-borne microorganisms. 100% of quinoa seeds, from different sources, are inhabited by diverse members of the genus Bacillus. These endophytes are motile and reside in all seedling organs, indicating vertical transmission. Owing to their high catalase activities and superoxide contents the bacteria potentially manipulate the host’s redox status. Superoxide-driven cell expansion enables quinoa to overcome a critical period in development, seedling establishment. Quinoa’s immediate confrontation with “foreign” reactive oxygen species and bacterial elicitors likely induces a naturally primed state, enabling plants to withstand extreme situations. The endophytic bacteria, which are cultivable and highly robust themselves, have high potential for application in agriculture, food (amylase) and cosmetics (catalase) industry. This work also discusses the potential of transferring quinoa’s microbiome to improve stress resistance in other plant species.
Insertion Mutagenesis and Membrane Topology Model of the Pseudomonas aeruginosa Outer Membrane Protein OprM

ABSTRACT Pseudomonas aeruginosa OprM is a protein involved in multiple-antibiotic resistance as the outer membrane component for the MexA-MexB-OprM efflux system. Planar lipid bilayer experiments showed that OprM had channel-forming activity with an average single-channel conductance of only about 80 pS in 1 M KCl. The gene encoding OprM was subjected to insertion mutagenesis by cloning of a foreign epitope from the circumsporozoite form of the malarial parasite Plasmodium falciparum into 11 sites. In Escherichia coli, 8 of the 11 insertion mutant genes expressed proteins at levels comparable to those obtained with the wild-type gene and the inserted malarial epitopes were surface accessible as assessed by indirect immunofluorescence. When moved to a P. aeruginosaOprM-deficient strain, seven of the insertion mutant genes expressed proteins at variable levels comparable to that of wild-type OprM and three of these reconstituted MIC profiles resembling those of the wild-type protein, while the other mutant forms showed variable MIC results. Utilizing the data from these experiments, in conjunction with multiple sequence alignments and structure predictions, an OprM topology model with 16 β strands was proposed.
Data-driven mechanistic analysis method to reveal dynamically evolving regulatory networks

Motivation: Mechanistic models based on ordinary differential equations provide powerful and accurate means to describe the dynamics of molecular machinery which orchestrates gene regulation. When combined with appropriate statistical techniques, mechanistic models can be calibrated using experimental data and, in many cases, also the model structure can be inferred from time–course measurements. However, existing mechanistic models are limited in the sense that they rely on the assumption of static network structure and cannot be applied when transient phenomena affect, or rewire, the network structure. In the context of gene regulatory network inference, network rewiring results from the net impact of possible unobserved transient phenomena such as changes in signaling pathway activities or epigenome, which are generally difficult, but important, to account for. Results: We introduce a novel method that can be used to infer dynamically evolving regulatory networks from time–course data. Our method is based on the notion that all mechanistic ordinary differential equation models can be coupled with a latent process that approximates the network structure rewiring process. We illustrate the performance of the method using simulated data and, further, we apply the method to study the regulatory interactions during T helper 17 (Th17) cell differentiation using time–course RNA sequencing data. The computational experiments with the real data show that our method is capable of capturing the experimentally verified rewiring effects of the core Th17 regulatory network. We predict Th17 lineage specific subnetworks that are activated sequentially and control the differentiation process in an overlapping manner. Availability and Implementation: An implementation of the method is available at http://research.ics. aalto.fi/csb/software/lem/. Contacts: jukka.intosalmi@aalto.fi or harri.lahdesmaki@aalto.fi
Biomechanical comparison of fixation of two-part osteoporotic neck fracture of the proximal humerus using uni-planar and multi-planar Kirschner wire.

OBJECTIVES The stability and effectiveness of uni-planar Kirschner wire (K-wires) was compared to multi-planar K-wires osteosynthesis combined with tension band wiring for fixation of two-part osteoporotic surgical neck fracture of the proximal humerus. MATERIALS AND METHODS Two groups each with eight cadaveric elderly (mean age 72.6; range 70 to 80 year) frozen human humeri were used in the study. Transverse osteotomy of the proximal humerus was performed using a thin oscillating saw. The first group (group A) was fixed using two anterograde smooth K-wires, sent from lateral cortex, combined with tension band wiring. The second group (group B) was fixed using multi-planar (anterograde and retrograde) four smooth K-wires combined with tension band wiring on the lateral cortex. Biomechanical tensile properties for 3 mm displacement (gap load) and maximum load were assessed. RESULTS The mean value for the gap load was 1045.0+/-45.4 N (Newton) for group A and 1238.1+/-115.8 N for group B. Gap load values of groups were similar (p=0.01). The maximum load was 1261.8+/-52.4 N in group A and 1471.1+/-107.3 N in group B. The maximum load values were statistically higher in the multiplanar fixation technique (group B) when compared to that of the uniplanar fixation technique (group A), (p=0.004). CONCLUSION Fixation in osteoporotic two-part surgical neck fractures of the proximal humerus using multiplanar K-wires combined with tension band wire provides substantially more effective stability compared to that of uniplanar fixation.
Virtual Performance Augmentation in an Immersive Jump & Run Exergame

Human performance augmentation through technology has been a recurring theme in science and culture, aiming to increase human capabilities and accessibility. We investigate a related concept: virtual performance augmentation (VPA), using VR to give users the illusion of greater capabilities than they actually have. We propose a method for VPA of running and jumping, based on in place movements, and studied its effects in a VR exergame. We found that in place running and jumping in VR can be used to create a somewhat natural experience and can elicit medium to high physical exertion in an immersive and intrinsically motivating manner. We also found that virtually augmenting running and jumping can increase intrinsic motivation, perceived competence and flow, and may also increase motivation for physical activity in general. We discuss implications of VPA for safety and accessibility, with initial evidence suggesting that VPA may help users with physical impairments enjoy the benefits of exergaming.
Intra-individual changes in body weight in population-based cohorts during four decades: the Finnish FINRISK study.

BACKGROUND The aim of the study was to evaluate trends in intra-individual weight changes over the last four decades in Finland. METHODS Within the eight FINRISK surveys conducted during the years 1972-2007, we identified individuals who had participated, by chance in at least two surveys. First, individuals aged 25-54 years who had undergone a health examination within 10 years of the first examination (n = 2033) were categorized into five cohorts covering different time periods, and the annual weight change was calculated at follow-up. Second, for each individual aged 25-69 years the longest possible follow-up time (5-35 years) was identified (n = 3443), and the corresponding annual weight change was evaluated. RESULTS Comparing the five cohorts from different time periods, the annual increase in body weight among men between 25- and 54-year old remained stable in the range of 0.27-0.47 kg per year over the decades, whereas women belonging to the most recent cohorts (the 1990s) gained weight at 0.53-0.63 kg per year, which is more than double the oldest cohort's weight gain of 0.24 kg. Overall, the annual increase in weight was around 0.3 kg in both sexes. The younger participants had a stronger tendency to gain weight than the older, and those with BMI < 25 kg/m(2) gained more than overweight or obese individuals. CONCLUSION The amount of intra-individual annual increase in body weight among men remained stable over the decades, while it increased among women. The tendency to gain weight was most pronounced among the youngest and among those initially leanest.
A Critique and Improvement of an Evaluation Metric for Text Segmentation

The Pk evaluation metric, initially proposed by Beeferman, Berger, and Lafferty (1997), is becoming the standard measure for assessing text segmentation algorithms. However, a theoretical analysis of the metric finds several problems: the metric penalizes false negatives more heavily than false positives, overpenalizes near misses, and is affected by variation in segment size distribution. We propose a simple modification to the Pk metric that remedies these problems. This new metriccalled Window Diffmoves a fixed-sized window across the text and penalizes the algorithm whenever the number of boundaries within the window does not match the true number of boundaries for that window of text.
More Ef cient Local Polynomial Estimation in Nonparametric Regression With Autocorrelated Errors

We propose a modi cation of local polynomial time series regression estimators that improves ef ciency when the innovation process is autocorrelated. The procedure is based on a pre-whitening transformation of the dependent variable that must be estimated from the data. We establish the asymptotic distribution of our estimator under weak dependence conditions. We show that the proposed estimation procedure is more ef cient than the conventional local polynomial method. We also provide simulation evidence to suggest that gains can be achieved in moderate-sized samples.
Formation of Complex Extrachromosomal T-DNA Structures in Agrobacterium tumefaciens-Infected Plants1[C][W][OA]

Agrobacterium tumefaciens is a unique plant pathogenic bacterium renowned for its ability to transform plants. The integration of transferred DNA (T-DNA) and the formation of complex insertions in the genome of transgenic plants during A. tumefaciens-mediated transformation are still poorly understood. Here, we show that complex extrachromosomal T-DNA structures form in A. tumefaciens-infected plants immediately after infection. Furthermore, these extrachromosomal complex DNA molecules can circularize in planta. We recovered circular T-DNA molecules (T-circles) using a novel plasmid-rescue method. Sequencing analysis of the T-circles revealed patterns similar to the insertion patterns commonly found in transgenic plants. The patterns include illegitimate DNA end joining, T-DNA truncations, T-DNA repeats, binary vector sequences, and other unknown “filler” sequences. Our data suggest that prior to T-DNA integration, a transferred single-stranded T-DNA is converted into a double-stranded form. We propose that termini of linear double-stranded T-DNAs are recognized and repaired by the plant’s DNA double-strand break-repair machinery. This can lead to circularization, integration, or the formation of extrachromosomal complex T-DNA structures that subsequently may integrate.