Miracle-dz/UniFAR-FTUs huggingface dataset:
In-situ single cell mechanical characterization of W303 Yeast cells inside Environmental-SEM

We present the environmental-SEM (ESEM)-nanomanipulator system for in-situ measurement of mechanical properties of the yeast cells (W303 strain). This enhanced ESEM system comprises of a standard ESEM instrument as a nano imaging tool, a cooling stage as a cellular biology's humidity controller and 7 D.O. F. linear actuators as nanomanipulator/effector. Two types of experiments have been conducted, i.e. mechanical properties of individual yeast cells and forces on cell-substrate area. Different kinds of spring constants (0.02 N/m, 0.09 N/m and 0.7 N/m) and tip's shapes (sharp, flat and needle-like) of the cantilevers have been used during the experiments. From the analysis, the compressed forces needed to penetrate the cell wall of the yeast cells using sharp and flat tips (0.02 N/m for both) are in the range of 87-278 nN and 57-207 nN respectively. Locality mechanical measurement has been performed using needle-like tip (0.09 N/m) on single-cell and mother-daughter cells where the elastic properties of the cells are in the range of 1.32-3.95 MPa. In addition to the above data, we have also investigated forces on cell-substrate area which can be divided into noncontact and contact forces. Under noncontact forces, average electrostatic forces between Au tip-Al substrate and tip-cell surfaces are measured to be 16 plusmn 2 nN and 5 plusmn 2 nN respectively. While under contact forces, two types of surface adhesions are measured which are cantilever's tip-wet surface adhesion and cell-surface adhesion where the release forces for each adhesion are 1107 plusmn 129 nN and 26578 nN respectively.
Lazy Factored Inference for Functional Probabilistic Programming

Probabilistic programming provides the means to represent and reason about complex probabilistic models using programming language constructs. Even simple probabilistic programs can produce models with infinitely many variables. Factored inference algorithms are widely used for probabilistic graphical models, but cannot be applied to these programs because all the variables and factors have to be enumerated. In this paper, we present a new inference framework, lazy factored inference (LFI), that enables factored algorithms to be used for models with infinitely many variables. LFI expands the model to a bounded depth and uses the structure of the program to precisely quantify the effect of the unexpanded part of the model, producing lower and upper bounds to the probability of the query.
Comparative Study of Fluoride-Tolerance of Five Typical Bioleaching Microorganisms

In the bioleaching of uranium ore, fluoride that ever accreted with the ore floats into solution, inhibiting the growth and metabolic processes of microorganism or even killing them, further reducing the efficiency of uranium leaching. In order to study the fluoride tolerance of the bioleaching microorganisms, five typical bioleaching strains including Acidithiobacillus ferrooxidans ATCC 23270, Leptospirillum ferriphilum YSK, Sulfobacillus thermosulfidooxidans ST, Acidithiobacills thiooxidans A01, Acidithiobacills caldus S1 were selected to compare their growth fluctuation and their oxidation rate of iron or sulfur in the presence of different concentration of fluoride. The results showed that At. ferrooxidans ATCC 23270 held the best fluoride tolerance, while S. thermosulfidooxidans ST took the worst. In order to explore the mechanism of microbial resistance to fluoride, whole-genome array (WGA) was used to analyze the genome-wide expression profiling of At. ferrooxidans ATCC 23270 upon 4.8 mM fluoride stress. The results showed that gene categories closely related to fluoride tolerance include cell membrane, energy metabolism, transport and binding functions of proteins, DNA metabolism, cell processing, synthesis and transportation of protein and other functional and metabolic pathways. Most of the genes associated with iron-sulfur metabolic system of At. ferrooxidans were highly expressed during 10 to 120 minutes, while in the long-term stress for 4 hours, the gene expression returned to normal level or even were down regulated. All these results provide useful information for further research on domesticating bacteria and increasing the efficiency of uranium leaching.
Beg, Borrow and Steal: Three Aspects of Horizontal Gene Transfer in the Protozoan Parasite, Cryptosporidium parvum

Cryptosporidium infection, or cryptosporidiosis, was first described in mice by Ernest Tyzzer in 1907, yet infection of humans went unrecognized until 1976 [1,2]. The emergence of HIV brought human cryptosporidiosis to the fore, in the 1980s, as a chronic and life threatening opportunistic infection. Most recently, a series of epidemiological studies have revealed the truly ubiquitous nature of cryptosporidiosis and its massive impact on global public health. Young children are highly susceptible to cryptosporidiosis, and in one of the recent epidemiological surveys—the Global Enteric Multicentre Study (GEMS)—cryptosporidiosis was found to be a major contributor to severe diarrheal disease in children under the age of two [3]. Severe cryptosporidiosis is closely associated with mortality, yet children who survive infections, even asymptomatic infections, can suffer from lasting growth and developmental defects [3–5]. Cryptosporidium parasites are environmentally hardy, withstanding common water treatments such as chlorination, and thus remain a major cause of waterborne outbreaks in industrialized countries as well [2]. Cryptosporidium belong to the eukaryotic phylum Apicomplexa, distant relatives of the parasites that cause malaria and toxoplasmosis. Although many species and strains of Cryptosporidium have been reported to infect humans, the majority of infections are caused by Cryptosporidium hominis and Cryptosporidium parvum. C. hominis and C. parvum are closely related, differing at the nucleotide level by 3%–5% [6,7]. Both of their genomes are small (approximately 9 Mb), adenosineand thymidine-rich (approximately 70%), and contain a relatively large proportion of genes acquired from other organisms by horizontal gene transfers (HGTs) [8]. HGTs have clearly had a significant influence on the evolution of Cryptosporidium, and here we will highlight just three: metabolism in an anaerobic environment, salvage of nucleotides from the infected host, and one HGT that may allow Cryptosporidium to evade host immunity.
Title of Proposal: Extending the Possibilities of Graph Theoretic Clustering and Segmenta- Tion: from Parallel Computing Expedition to Interdisciplinary Applications

of Proposal: Graph theoretic clustering and segmentation has been widely used and proved to be a powerful tool. It has intuitive mathematical representation and no requirement for the prior knowledge. The results are usually better than other algorithms but the graph based algorithms are also computationally heavy. There are some parallelized algorithms based on the Graphics Processor Unit (GPU) parallel computing framework CUDA but some newly developed algorithms doesn't have their parallelized correspondents. In addition, some parallelized graph theoretic algorithms newly proven to be efficient are not widely used in imaging science. Based on the history of mutual inspiration of interdisciplinary research related to imaging science, we proposed to extend the current application of the latest graph theoretic algorithms, especially the parallelized expedited versions, to a wider range in imaging science. This includes a series of hierarchical objectives: 1)The application of latest parallelized graph based clustering on the hyperspectral remote sensed data or color image segmentation based on CUDA or OpenCL; 2)The parallelized transplant of the latest graph based clustering algorithms based on CUDA; 3)Conduct a pilot study to explore the potential extension of applications of graph theoretic clustering across different application scenarios/disciplines within the area of imaging science. Through these steps, newly proposed parallelism algorithms are expected to expedite the clustering of large volume of hyperspectral data, or even more, to achieve mutual benefits of subfields of imaging science who intensively use clustering and segmentation techniques.
Feasibility of interference alignment for the MIMO interference channel: The symmetric square case

Determining the feasibility conditions for vector space interference alignment in the K-user MIMO interference channel with constant channel coefficients has attracted much recent attention yet remains unsolved. The main result of this paper is restricted to the symmetric square case where all transmitters and receivers have N antennas, and each user desires d transmit dimensions. We prove that alignment is possible if and only if the number of antennas satisfies N ≥ d(K + 1)/2. We also show a necessary condition for feasibility of alignment with arbitrary system parameters. An algebraic geometry approach is central to the results.
Functional Analysis of Effector and Regulatory T Cells in a Parasitic Nematode Infection

ABSTRACT Parasitic nematodes typically modulate T-cell reactivity, primarily during the chronic phase of infection. We analyzed the role of CD4-positive (CD4+) T effector (Teff) cells and regulatory T (Treg) cells derived from mice chronically infected with the intestinal nematode Heligmosomoides polygyrus. Different CD4+ T-cell subsets were transferred into naïve recipients that were subsequently infected with H. polygyrus. Adoptive transfer of conventional Teff cells conferred protection and led to a significant decrease in the worm burdens of H. polygyrus-infected recipients. Roughly 0.2% of the CD4+ T cells were H. polygyrus specific based on expression of CD154, and cells producing interleukin 4 (IL-4) and IL-13 were highly enriched within the CD154+ population. In contrast, adoptive transfer of Treg cells, characterized by the markers CD25 and CD103 and the transcription factor Foxp3, had no effect on the worm burdens of recipients. Further analysis showed that soon after infection, the number of Foxp3+ Treg cells temporarily increased in the inflamed tissue while effector/memory-like CD103+ Foxp+ Treg cells systemically increased in the draining lymph nodes and spleen. In addition, Treg cells represented a potential source of IL-10 and reduced the expression of IL-4. Finally, under in vitro conditions, Treg cells from infected mice were more potent suppressors than cells derived from naïve mice. In conclusion, our data indicate that small numbers of Teff cells have the ability to promote host protective immune responses, even in the presence of Treg cells.
Experimental study on natural circulation using liquid nitrogen for superconducting applications

An experiment to investigate the natural circulation of a cryogen has been performed. The study is motivated mainly by our recent development of cryogenic cooling system for prototype superconducting cyclotron without any circulating pump. In the natural circulation loop system, a cooling channel is attached on the outer surface of the aluminium block and the liquid nitrogen passes through inside of the channel to cool the block indirectly. A cryocooler as a heat sink is located at the top to re-condense cryogenic vapor coming from the aluminium block in which electrical heater is installed as a heat source. The main dimensions are determined using the relevant analysis and the natural circulation loop is successfully fabricated. The temperature distributions in the loop are measured during initial cool-down process and in steady state, from which the modified Grashof numbers are calculated and compared with the existing correlation estimated with one-dimensional analysis for steady state flow.
Degeneration and regeneration of the intervertebral disc: lessons from development

Degeneration of the intervertebral discs, a process characterized by a cascade of cellular, biochemical, structural and functional changes, is strongly implicated as a cause of low back pain. Current treatment strategies for disc degeneration typically address the symptoms of low back pain without treating the underlying cause or restoring mechanical function. A more in-depth understanding of disc degeneration, as well as opportunities for therapeutic intervention, can be obtained by considering aspects of intervertebral disc development. Development of the intervertebral disc involves the coalescence of several different cell types through highly orchestrated and complex molecular interactions. The resulting structures must function synergistically in an environment that is subjected to continuous mechanical perturbation throughout the life of an individual. Early postnatal changes, including altered cellularity, vascular regression and altered extracellular matrix composition, might set the disc on a slow course towards symptomatic degeneration. In this Perspective, we review the pathogenesis and treatment of intervertebral disc degeneration in the context of disc development. Within this scope, we examine how model systems have advanced our understanding of embryonic morphogenesis and associated molecular signaling pathways, in addition to the postnatal changes to the cellular, nutritional and mechanical microenvironment. We also discuss the current status of biological therapeutic strategies that promote disc regeneration and repair, and how lessons from development might provide clues for their refinement.
A Lagrangian heuristic for bid evaluation in e-procurement auctions

e-Procurement is an Internet based business process for sourcing direct or indirect materials. This paper considers a procurement scenario of a buyer procuring large quantities of a single good. The suppliers submit nonconvex piecewise linear supply curves as their bids. Such bids enable the suppliers to effectively express their economies of scale and transportation constraints. The buyer imposes a business rule of limiting the winning suppliers within a preferred range. The bid evaluation problem faced by the buyer is to select the winning suppliers and their trading quantities, such that the cost of procurement is minimized while satisfying the supply, demand, and business constraints. The bid evaluation problem is NP-hard even for a simple special case. In this paper, the problem is formulated as a mixed integer linear programming problem and we propose a Lagrangian relaxation based heuristic to find a near optimal solution. The computational experiments performed on representative data sets show that the proposed heuristic produces a feasible solution with negligible optimality gap.
Immune rejection of Trichostrongylus colubriformis in sheep; a possible role for intestinal mucus antibody against an L3‐specific surface antigen

Sheep that have been immunized by multiple truncated infections with the parasitic nematode Trichostrongylus colubriformis contain anti‐larval activity in their intestinal mucus and high‐speed mucus supernatants. This activity induces T. colubriformis L3 to clump in vitro and causes a significant reduction in larval establishment in naive sheep after infusion of larvae and mucus into the intestinal lumen via a duodenal cannula. In this report, we provide evidence that one factor contributing to the anti‐larval activity of immune mucus is antibody against a 35‐kDa L3‐specific cuticular antigen. The anti‐larval activity in mucus is > 100 kDa by membrane filtration, is heat labile and sensitive to either protease digestion or reduction with DTT. Immunoblotting showed that mucus and supernatants of ultracentrifuged mucus from immune sheep contained IgG1 and IgA antibodies that recognized predominantly a larval antigen with an estimated molecular weight of 35 kDa on SDS‐PAGE. Antibodies eluted from the surface of washed larvae that had been incubated in immune mucus also reacted specifically with the 35 kDa antigen on blots of larval homogenate. Immunofluorescence and immunogold electron microscopy showed that the 35 kDa antigen is present on the epicuticle of L3 and is shed during the moult to L4. The antigen is not present in eggs, L1, L2, L4 or adult worms and is found only in extracts of sheaths and L3 before infection and up to 4 days after infection. We hypothesize that the binding of antibody to the larval surface prevents larvae from establishing at their preferred site, causing them to be eliminated from the intestine. Monoclonal antibody PAB‐1 recognizes the 35 kDa T. colubriformis larval antigen and also cross‐reacts with antigens of similar molecular weight on blots of L3 extracts of the parasitic nematodes Haemonchus contortus and Ostertagia circumcincta; and with a 22‐kDa antigen on blots of L3 extracts from Cooperia curticei and Nematodirus spathiger. This indicates that an antigenically related surface antigen with immunizing potential is present on several nematode species and can be identified by mAb PAB‐1. The 35 kDa T. colubriformis larval antigen and related molecules in other nematodes are potential novel targets for stimulating host‐protective immunity against nematode infections.
Biobased Fillers for Polypropylene for Interior Application

Coconut shells and torrefied wood are bio-sourced and renewable materials that can be used as fillers in various polymer matrices. These bio-fillers would replace talc and glass bubbles which are not a renewable resource. The implementation of torrefied wood and coconut would reduce the carbon footprint and improve sustainability of Hyundai and Kia vehicles. In this study, coconut and torrefied wood filled polypropylene properties are tested for a HVAC Case application. Weight savings (7-10%) achieved by replacing talc with coconut or torrefied wood. Lower coconut and torrefied wood concentration (10-20%) is preferred for optimum of mechanical properties.
Current Status of HIV/AIDS in Cameroon: How Effective are Control Strategies?

Nearly three decades after its discovery, HIV infection remains the number one killer disease in Sub-Saharan Africa where up to 67% of the world’s 33 million infected people live. In Cameroon, based on a Demographic Health Survey carried out in 2004, the national HIV prevalence is estimated at 5.5% with women and youths being predominantly infected. Orphans and vulnerable children (OVC) from the HIV and AIDS pandemic have increased steadily over the years; hospital occupancy is estimated at about 30%, hence stretching the health system; co-infections like HIV/tuberculosis have been reported to reach 40–50% of infected cases and 95% of teachers are said not to be productive on several counts. Thus, the impact is multi-sectorial. Furthermore, the HIV epidemic in Cameroon is peculiar because of the wide HIV-1 genetic diversity of HIV-1 Group M observed with several subtypes reported (A, B, C, D, F, G, H, J, K), predominantly subtype A. There are also circulating recombinant forms, mainly CRF02_AG. In addition, HIV-1 Groups O and N have all been noted in Cameroon. These findings have great implications not only for HIV diagnosis, but also for responsiveness to therapy as well as for vaccine development. In 1986, the initial response of the Cameroon government to the increasing trends in the HIV/AIDS infection was to create a National AIDS Control Committee to coordinate a national AIDS programme. By 2000, the first National Strategic Plan was drawn for 2000–2005. The second National Strategic Plan for 2006–2010 is currently being implemented and covers various axes. Some results obtained show that there has been significantly positive outcomes noted in the various arms of intervention by the Cameroon government.
Probabilistic Explanation Dialog Augmentation

Human-computer trust (HCT) is an important factor influencing the complexity and frequency of interaction in technical systems. Especially incomprehensible situations in human-computer interaction (HCI) may decrease the user's trust and through that the way of interaction. However, analogous to human-human interaction (HHI), providing explanations in these situations can help to remedy negative effects. In this paper, we present our approach of augmenting task-oriented dialogs with selected explanation dialogs to stabilize the HCT relationship. We conducted a study comparing the effects of different explanations on HCT. These results were used in a probabilistic trust handling architecture to augment pre-defined task-oriented dialogs.
Obesity, poor muscle strength, and venous thromboembolism in older persons: the InCHIANTI study.

BACKGROUND Both obesity and the decline in muscle strength, which often occur with aging, are accompanied by functional and metabolic changes that may affect the risk of thrombosis. This study evaluated whether obesity and poor muscle strength are associated with venous thromboembolism (VTE). METHODS Objectively confirmed VTEs were assessed at baseline and more than a 6-year follow-up in 1,045 participants more than or equal to 60 years enrolled in the InCHIANTI study. RESULTS At baseline, 97 participants had a positive history of VTE. Obese participants were almost twice more likely (odds ratio 1.76; 95% confidence interval 1.03-3.01) and obese with poor muscle strength were threefold more likely (odds ratio 2.99; 95% confidence interval 1.56-5.73) to have VTE compared with lean participants with normal strength. Fifty-five VTEs occurred during follow-up. History of VTE, obesity, and/or poor strength independently predicted new VTE events. In participants with previous VTE, the odds ratio (95% confidence interval) for thrombosis was 6.64 (1.92-22.95) with poor strength, 9.69 (3.13-30.01) in the obese, and 14.57 (5.16-41.15) in the obese with poor strength as compared with lean participants with normal strength. CONCLUSION Obesity with or without poor muscle strength is a risk factor for VTE among older persons and significantly amplifies the risk of recurrent thrombosis.
Event-Centered Information Retrieval Using Kernels on Event Graphs

Traditional information retrieval models assume keyword-based queries and use unstructured document representations. There is an abundance of event-centered texts (e.g., breaking news) and event-oriented information needs that often involve structure that cannot be expressed using keywords. We present a novel retrieval model that uses a structured event-based representation. We structure queries and documents as graphs of event mentions and employ graph kernels to measure the query-document similarity. Experimental results on two event-oriented test collections show significant improvements over state-ofthe-art keyword-based models.
A physiological basis for two group, healthy male voicing identified using spectral approximate entropy

December 13-15, 2007: Firenze, Italy, ed. by C. Manfredi, ISBN 978 88-8453-673-3 (print) ISBN 978-88-8453-674-7 (online) © Firenze university press, 2007. Abstract: The approximate entropy of vowel phonation spectra has been used to reveal two normal voicing groups in healthy males. An analysis of the corresponding open and closed quotients for the groups shows the first with balanced quotients and the second with asymmetric quotients characterised by pronounced vocal fold open phases. This indicates the second group is impacted by turbulent air flow, which reduces both the spectral structure in and approximate entropy of vowel phonation. The corresponding spectra are presented to confirm the effect. This provides a physiological explanation for the success of approximate entropy as a single figure of merit for voicing quality.
Future of CMOS technology

Previously, CMOS downsizing has been accelerated very aggressively in both production and research level, and even transistor operation of a 5 nm gate length p-channel MOSFET was reported in a conference. However, many serious problems are expected for implementing small-geometry MOSFETs into large scale integrated circuits even for 45 nm technology node, and it is questionable whether we can successfully introduce sub-10 nm CMOS LSIs into market or not. In This work, limitation and its possible causes for the downscaling of CMOS are discussed from many aspects.