Miracle-dz/UniFAR-FTUs huggingface dataset:
Investigating functions of tumor-infiltrating natural killer cells in genetically-engineered mouse models of non-small cell lung cancer

The immune system has long been hypothesized to play a role in restraining tumor growth, but compelling evidence for this role evaded scientists for the better part of a century. After many years of skepticism, the field of cancer immunology has recently undergone a major revolution. The success of modern immunotherapeutics has transformed the arenas of oncology and drug development. Large efforts are now focused on understanding the factors that dictate patient responses to immunotherapy, for the identification of possible points of intervention to expand the fraction of patients who benefit from therapy. The majority of approved immunotherapeutics directly target adaptive immune effectors. However, emerging evidence suggests that these treatments preferentially benefit patients with pre-existing immune responses against tumors, and patients who fail therapies often harbor tumors that are poorly infiltrated by adaptive immune cells. I have explored the role of an innate immune effector known for its capacity to kill tumor cells and its importance in stimulating and shaping adaptive immune responses, the natural killer (NK) cell. To this end, I developed a new system for assaying NK cell function in the context of established, autochthonous lung cancer, by engineering vectors for producing tumors with inducible NK cell activating ligands. Using this model, I have shown that NK cells in established tumors exhibit dysfunctional phenotypes, but their responses can be boosted by providing activating stimuli. Strikingly, stimulation of NK cells results in the recruitment of adaptive immune cells to tumors. By developing a next-generation model for inducing activating NK cell ligands in tumors engineered to express T cell antigens, I demonstrated that NK cell activation in immunogenic tumors results in effective immune responses that restrain tumor growth, highlighting the potential for cooperation between innate and adaptive arms of the immune system in anti-tumor immunity. Finally, I developed a novel immunotherapeutic molecule for stimulating NK cell responses against cancer cells. Bifunctional molecules are an emerging class of anti-cancer agents, designed to target immune effectors against tumors. I produced and performed initial functional testing on a bifunctional molecule that stimulates NK cell responses against tumors by 'decorating' the surface of cancer cells with activating NK cell ligands. I demonstrated that this bifunctional molecule induces NK cell cytotoxicity against tumor targets. Based on this work, we hypothesize that strategies for stimulating NK cells in tumors may enhance the efficacy of T cell-targeted therapies in the treatment of cancer. Thesis supervisor: Tyler Jacks Title: Professor of Biology 3 Leah Marie Schmidt schmidtl@mit.edu Koch Institute at M.I. T. 76-453 77 Massachusetts Avenue, MA 02139 Education:
Monitoring and significance of the recessive genetic defect AH1 of Ayrshire cattle

Modern dairy farming is characterised by high selection intensity and the use of a limited number of bulls-producers. This increases the likelihood of widespread genetic defects in livestock populations. Genome-wide studies have identified DNA loci associated with the disruption of foetal embryonic development and its death, which have been called “fertility haplotypes”. The aim of this study is to analyse the occurrence of АН1 haplotype or rs475678587 in Ayrshire bulls (n = 186) used in the artificial insemination system of Russia and to evaluate the reproductive and productive qualities of their daughters. The proportion of genetic defect carrier bulls in the analysed sample cohort was 16.66%. Analysis of the proportion of carriers of unwanted haplotype depending on the place of birth of the bull for service showed that the highest frequency was observed in bulls of Canadian origin (26.66%). Based on data on 97 478 cow and heifer calvings, stillbirth and abortion rates were analysed and cow reproduction rates were based on an AH1 status for the bull-father and bull for service. We observed a significant increase (P < 0.05 and P < 0.001) in the incidence of stillbirths when crossing the daughters of AH1-C bulls with AH1-C bulls. There was no negative association of abortion rates and reproductive qualities with AH1 haplotype. The high incidence of AH1 haplotype among animals of Ayrshire breed requires regular screening for the carriers of this haplotype not only among bulls, but also in cows.
Li poprotein-c h fed defined diets from ages 1 to 12 months: comparison of diets predominant in oleic acid versus linoleic acid, with para1 infants fed a human milk- rol responees in healthy infants

A prospective study in healthy infants predefining both diet fatty acid and cholesterol, from birth to age 1 year, compared response of cholesterol fractions in three groups: ran- dom assignment to 1) monounsaturated-(Hi-Mono) (n = 20), or 2) polyunsaturated-(Hi-Poly) (n = 22) fatty acid-enriched diets, or 3) non-randomized selection to breast feeding (Human Milk) (n = 25). In each group, designated weaning foods and supplements maintained fatty acid and cholesterol intake similar to that of each group's defined formulas, with long-term compli- ance confirmed by plasma phospholipid fatty acid concentra- tions. By 12 months, total cholesterol was significantly lower in the Hi-Poly group compared to either of the other groups (P < 0.05). Low density lipoprotein (LDL)- and high density lipoprotein (HDL)-cholesterol concentrations were significantly lower by 12 months in the Hi-Poly group, compared to the Hi- Mono groups. However, at the earlier 4-month interval, total cholesterol and LDL-cholesterol in both Hi-Mono and Hi-Poly groups were not different from each other, although each was significantly lower than the parallel Human Milk-group (P < 0.05). The Hi-Mono group increased gradually in total and LDL-cholesterol such that, after 12 months' feedings, all lipid fractions of this Hi-Mono group were no different from those of the Human Milk group. In independent group compar- isons, there were no significant differences in HDL-cholesterol concentrations after 4 and 9 months on these diets. Independent of diet, HDL-cholesterol showed a falling trend as an overall time-effect across all groups (P < 0.001). These data sug- gest that prolonged feeding of a diet enriched in polyunsaturated acids in early infancy has a significant cholesterol-lowering effect compared to monounsaturates. These differences in total, LDL-, and HDL-cholesterol plasma concentrations between polyun- saturates and monounsaturates were not significantly evident until feedings had continued for a year. -Mize, C. E. , R. Uauy, R. Kramer, M. Benser, S. Allen, and S. M. Grundy. Lipoprotein-cholesterol responses in healthy infants fed defined diets from ages 1 to 12 months: comparison of diets predominant in oleic acid versus linoleic acid, with parallel observations in in- fants fed a human &-based diet.J Lijndh. 1995. 36 1178-1187.
Flavor Thresholds of Polyphenolics in Water

Taste thresholds of polyphenolics in deionized water were determined by the ascending method of limits. For procyanidins based upon (+)-catechin units the threshold depended upon their degree of polymerization. Both caffeine (1.5 mmol/L) and quinine sulfate (18 µmol/L) suppressed the taste sensation of a procyanidin fraction containing mainly trimeric and tetrameric procyanidins. In all test samples, the threshold value of this same fraction was lower when the weight content of polyphenolics was raised by one third by adding (+)-catechin.
Molecular characterization of Humicola grisea isolates associated with Agaricus bisporus compost

Composite compost samples were collected from Solan, Sonepat, Gangtok, Kaithal, Phagwara and Ooty, at different stages of Agaricus bisporus compost preparation by long and short methods using a variety of agro-waste substrates. Eight isolates of Humicola grisea were retrieved on yeast agar medium at 45 and 52°C. PCR amplification of internal transcribed spacer (ITS) region of 5.8S ribosomal RNA (rRNA) gene was done using ITS-1 and ITS-4 primers. An ITS fragment of approximately 550 bp was amplified from all the eight H. grisea isolates with no intra-specific diversity in the ITS region of 5.8S rRNA gene. RAPD genotyping was performed using five decamer primers. Combined phylogenetic analysis of RAPD profiles of H. grisea by five primers depicted intra-specific variation amongst the eight isolates and divided these into five distinct sub-clades. Molecular analysis carried out in the present study would suggest that isolates within this species exhibit genetic differences, which correlates well with morphological variations.
Skipped-Hierarchical Feature Pyramid Networks for Nuclei Instance Segmentation

Dealing with multiple scale of object is main problem in computer vision. Feature Pyramid Networks (FPN) has widely used in instance segmentation area to utilize multiple scales of features. Using different scale of feature maps, the method enables to capture a various sizes of objects in a scene. However, FPN still cannot propagate semantic information of deeper layer into the shallow layer which contains spatial information strongly. In this paper, we propose a novel network which consists of stage residual connection and aggregation between $\boldsymbol{C_{i}}$ and $\boldsymbol{P}_{\boldsymbol{i}-1}$ above the FPN to improve the imperfectness of original FPNs for the instance segmentation. Our proposed network is called Skipped-Hierarchical Feature Pyramid Networks (SH-FPN), integrated on Mask R-CNN. Experimental results of SH-FPN show that it has significant improvement on Data Science Bowl 2018 benchmark dataset on nuclei segmentation, compared to FPN.
Accuracy evaluations of contact-free heart rate measurement mehods using 4K facial images

Recently, with the spread of Internet of Things (IoT), video surveillance system is widely used to detect abnormal activity using cameras and sensors. In such video surveillance system, contact-free heart rate measurement is a highly required technology to predict the occurrence of abnormal activities and suspicious humans. In this paper, our main contributions can be summarized by two aspects. First, we compare the accuracy performance of heart rate measurement using six heart beat waveform acquisition methods and two heart rate calculation methods. Second, we discuss the influence of image resolutions of RGB cameras on accurate performance, to investigate the requirement of surveillance cameras in actual scenarios.
FOOD CONCENTRATION AND TEMPERATURE EFFECTS ON LIFE CYCLE CHARACTERISTICS OF TROPICAL CLADOCERA (Daphnia gessneri Herbst, Diaphanosoma sarsi Richard, Moina reticulata (Daday)): I. DEVELOPMENT TIME

The effects of food concentration and temperature on embryonic and postem-bryonic duration of three tropical species, Daphnia gessneri(1.5mm), Diaphanosoma sarsi(1.2mm) and Moina reticulata(0.8mm), were investigated as part of life cycle studies which included growth, body size and reproduction. These are the very first experimental studies undertaken on these species. The long-term growth experiments were performed under controlled laboratory conditions at all combinations of temperature (22"C, 27"C and 32"C) and constant food concentration (0.03, 0.05, 0.10, 0.25, 0.50 and 1.00 mgC/L) of the unicellular green alga Scenedesmus acutus.Animals were examined twice daily throughout their life cycle from the neonate to third adult instar. In all three species, temperature exerted the most powerful influence on embryonic duration but there was also a smaller food effect. In D. gessneri,postembry-onic durations remained more or less the same at food levels 0.25 mgC/L but were influenced by temperature. At food concentrations of 0.1 mgC/L or lower, postembryonic durations became increasingly prolonged, particularly at high temperatures. This threshold concentration is affected by temperature: in D. gessneri,it was 0.1 mgC/L at 22oC and 27oC but higher at 32oC (between 0.25 and 0.50 mgC/L). At the same temperature of 27oC, the food threshold level varied between species: it was higher (0.25 mgC/L) for D. sarsiand lower (0.05 mgC/L) for M. reticulatacompared with D. gessneri(0.1 mgC/L). In both embryonic and postembryonic durations there is a body size effect as the absolute durations were longest in the largest species and shortest in the smallest species In all three species, prolongation of postembryonic duration at combinations of high temperature and lowered food levels was accompanied by increased number of juvenile instars.
Ants, plant characteristics and habitat conservation status affect the occurrence of myrmecophilous butterflies on an extrafloral nectaried Malpighiaceae

ABSTRACT We investigated the occurrence of myrmecophilous florivorous lycaenid larvae in Banisteriopsis malifolia (Malpighiaceae) according to habitat conservation status (disturbed and preserved savanna), plant phenology, height and the presence of tending ants. The abundance and richness of lycaenids were sixfold and fivefold greater, respectively, in the disturbed area than in the protected savanna. Lycaenids occurred mostly on plants visited by Camponotus blandus, a mutualistic partner of larvae. Habitat type was the main factor influencing lycaenid occurrence, as plants in open areas offered more food resources and tending ants. Banisteriopsis malifolia was considered useful as a host for lycaenids in disturbed sites.
Using Plant–Animal Interactions to Inform Tree Selection in Tree-Based Agroecosystems for Enhanced Biodiversity

The Neotropical region harbors the world’s most diverse terrestrial plant communities. A key component of this diversity is a range of plant– animal interactions involving frugivory, nectarivory, and insectivory. Millions of Neotropical hectares subjected to human land-use systems contain trees that are either planted by land managers or retained from the pre-existing forests. Biodiversity-conservation approaches in these systems are often ineffective because of the unfounded assumption that all plants provide equal benefits for consumers. We propose criteria for tree-species selection based on plant–animal interaction research that could guide decisionmakers. We show that tree-species identity is key for enhancing biodiversity and recommend that selection be guided by the structure of plant–animal interaction networks. We also recommend that selection practices consider the timing of resource production, because the year-round availability of food resources in the Neotropics plays an important role in the adaptive radiation of nectarand fruit-eating vertebrates.
Balanced harvesting is the bioeconomic equilibrium of a size‐structured Beverton‐Holt model

&NA; Balanced harvesting (BH) was introduced as an alternative strategy to size‐at‐entry fishing with the aim of maintaining ecosystem structure and functioning. BH has been criticized on a number of grounds, including that it would require an infeasible level of micromanagement and enforcement. Recent results from a size‐spectrum model show that the distribution of fishing mortality across body sizes that emerges from the behaviour of a large number of fishing agents corresponds to BH in a single species. Size‐spectrum models differ from classical size‐structured models used in fisheries as they are based on a bookkeeping of biomass transfer from prey to predator rather than a von Bertalanffy growth model. Here we investigate a classical Beverton‐Holt model coupled with the Gordon‐Schaefer harvesting model extended to allow for differential fishing pressure at different body sizes. This models an open‐access fishery in which individual fishing agents act to maximize their own economic return. We show that the equilibrium of the harvesting model produces an aggregate fishing mortality that is closely matched to the production at different body sizes, in other words BH of a single species. These results have significant implications because they show that the robustness of BH does not depend on arguments about the relative production levels of small versus large fish.
The effect of light intensity on the production of oat (Avena sativa L.) doubled haploids through oat × maize crosses

Oat haploid embryos were obtained by wide crossing with maize. The effect of light intensity during the growing period of donor plants (450 and 800 μmol m−2 s−1) and in vitro cultures (20, 40, 70 and 110 μmol m−2 s−1) was examined for the induction and development of oat DH lines. Oat florets (26008) from 32 genotypes were pollinated with maize and treated with 2,4-dichlorophenoxyacetic acid. All the tested genotypes formed more haploid embryos when donor plants were grown in a greenhouse (9.4%) compared to a growth chamber (6.1%). The light intensity of 110 μmol m−2 s−1 during in vitro culture resulted in the highest percentage of embryo germination (38.9%), conversion into plants (36.4%) and DH line production (9.2%) when compared with lower light intensities (20, 40 and 70 μmol m−2 s−1). The results show that the growth conditions of the donor plant and light intensity during in vitro culture can affect the development of haploid embryos. This fact may have an impact on oat breeding programs using oat × maize crosses.
Big data for forecasting the impacts of global change on plant communities

Aim Plant distributions and vegetation dynamics underpin key global phenomena, including biogeochemical cycling, ecosystem productivity and terrestrial biodiversity patterns. Aggregated and remotely collected ‘big data’ are required to forecast the effects of global change on plant communities. We synthesize advances in developing and exploiting big data in global change plant ecology, and identify challenges to their effective use in global change studies. Location Global. Methods We explored databases, catalogues and registries with respect to their accessibility, geographical and taxonomic extent, sample bias and other types of uncertainty, from the perspective both users and contributors. We identified four kinds of big data needed to predict the impacts of global change on plant populations and communities using spatially explicit models: remotely sensed and other environmental maps, species occurrence records, community composition (plots) and species traits, especially demographics. Results Digital environmental maps, including remotely sensed data, are the most mature class of big data discussed herein whereby protocols for archiving, discovering and analysing them have developed over three decades. Species locality records are being aggregated into databases that are easy to search and access, and while methods for addressing uncertainties are a major research focus, better spatial representation is still needed. Plot data from inventories have tremendous potential for monitoring and modelling the impacts of global change on plant communities but tend to be restricted to forests or concentrated in certain geographical areas. Ongoing efforts to aggregate plot and trait data from multiple sources are challenged by their heterogeneous coverage, attributes and protocols and a lack of data standards. Main conclusions Future goals include developing systematic frameworks for selecting geospatial data, improving tools for assessing the quality of species occurrence records and increased aggregation and discoverability of plot and trait data. Aggregated data collected by scientists, not sensors, provide more meaningful insights when data collectors are involved in analysis.
3D Scanning of High Dynamic Scenes Using an RGB-D Sensor and an IMU on a Mobile Device

With the development of RGB-D sensors and mobile devices, 3D scanning has witnessed great progress in recent years. KinectFusion opens up an era of RGB-D 3D reconstruction, which integrates captured depth images into a voxel-based representation. A number of improvements have been applied to the KinectFusion to reduce large footprint and make the 3D reconstruction on mobile devices possible. However, these methods are designed to handle static scenes. In this paper, we propose a method which can perform the 3D scanning of high dynamic scenes using an RGB-D sensor and an inertial measurement unit (IMU) on a mobile device. We first introduce a novel method to segment the depth images into static and dynamic elements with the use of sparse optical flow and the rotational part of the IMU. Then, we determine the camera pose with pixels labeled as static. At last depth, images are integrated into a voxel-based representation. The truncated signed distance function values of static voxels are updated while dynamic voxels are set to free-space. The experiments show that compared with some state-of-the-art systems, our method has better results when scanning high dynamic scenes and has comparable results when scanning low dynamic and static scenes. Besides, our method processes eight frames/s on an Apple iPad Air 2.
A Cluster Management Method for Heterogeneous Vehicular Networks

In this paper, we propose a cluster management method to shorten the data latency for heterogeneous vehicular networks. The proposed method introduces a secondary cluster head (CH) in addition to the primary CH to shorten the handover time of CHs. When a primary CH moves out of a cluster, the secondary CH seamlessly takes over. Via computer simulations, we confirm that the proposed method effectively shortens the data latency in cluster-based heterogeneous vehicular networks.
Screening of Preliminary Phytochemical Analysis and Antibacterial Activity of (Calotropis gigantea L. And Datura metel L.) Against Selected Pathogenic Microorganisms

Several hundreds of plant genera are used medicinally and plants are vital sources for potent and powerful drugs. Plants are exploited as medicinal source since ancient age. The traditional and folk medicinal system uses the plant products for the treatment of various infectious disease. About 75%of the Indian population relies heavily on the use of herbal drugs for the treatment of diseases. Medicinal herbs have a long history in improving human health and curing various diseases. A wide interest has been made for researchers using herbal material in identification of the active components and verification of their efficiency. Many researches are working seriously to find out substitutes for antibiotics as they cause side effects on the functioning of different parts of the body, organs and systems over the last twenty years. Ethno botanical and ubiquitous plants provide a rich resource for natural drug research and development. In the present investigation, the phytochemical and antibacterial activity of Calotropis gigantea and Datura metel. Solvent used Chloroform, Acetone and Ethanol antibacterial activity maximum in Calotropis gigantea against Staphylococcus aureus Escherichia coli, Salmonella spp, Klebsiella spp, compared to Datura metel. Synergism between plant extract and synthetic antibiotics can develop standardization of herbal medicine for treatment and prevention of infectious diseases.
Accelerating GPU Computing at Runtime with Binary Optimization

Nowadays, many applications use GPUs (Graphics Processing Units) to achieve high performance. When we use GPU servers, the idle CPU resource of the servers is often ignored. In this paper, we explore the idea: using the idle CPU resource to speed up GPU programs. We design a dynamic binary optimization framework for accelerating GPU computing at runtime. A template-based binary optimization method is proposed to optimize kernels, which can avoid the high cost of kernel compilation. This method replaces determined variables with constant values and generates an optimized binary kernel. Based on the analysis results of optimization opportunities, we replace the original kernels with optimized kernels during program execution. The experimental results show that it is feasible to accelerate GPU programs via binary optimization. After applying binary optimization to five convolution layers of deep neural networks, the average performance improvement can reach 20%.