Miracle-dz/UniFAR-FTUs huggingface dataset:
Single-cell time-series mapping of cell fate trajectories reveals an expanded developmental potential for human PSC-derived distal lung progenitors

Alveolar epithelial type 2 cells (AEC2s) are the facultative progenitors responsible for maintaining lung alveoli throughout life, yet are difficult to access from patients for biomedical research or lung regeneration applications. Here we engineer AEC2s from human induced pluripotent stem cells (iPSCs) in vitro and use single cell RNA sequencing (scRNA-seq) to profile the detailed kinetics of their differentiation over time. We focus on both the desired target cells as well as those that appear to diverge to alternative endodermal fates. By combining scRNA-seq with lentiviral barcoding to trace differentiating clones, we reveal the bifurcating cell fate trajectories followed as primordial lung progenitors differentiate into mature AEC2s. We define the global transcriptomic signatures of primary developing human AEC2s from fetal through adult stages in order to identify the subset of in vitro differentiating cells that appear to recapitulate the path of in vivo development. In addition, we develop computational methods based on Continuous State Hidden Markov Models (CSHMM) to identify the precise timing and type of signals, such as over-exuberant Wnt responses, that induce some early multipotent NKX2-1+ progenitors to lose lung fate as they clonally diverge into a variety of non-lung endodermal lineages. Finally, we find that this initial developmental plasticity is regulatable via Wnt modulation, and subsides over time, ultimately resulting in iPSC-derived AEC2s that exhibit a stable phenotype and nearly limitless self-renewal capacity in vitro. Our methods and computational approaches can be widely applied to study and control directed differentiation, producing an inexhaustible supply of mature lineages, exemplified here by the generation of AEC2s.
Translational efficiency across healthy and tumor tissues is proliferation‐related

Background Different tissues express genes with particular codon usage and anticodon tRNA repertoires. However, the codon-anticodon co-adaptation in humans is not completely understood, as well as its effect on tissue-specific protein levels. Results We first validated the accuracy of small RNA-seq for tRNA quantification across five human cell lines. We then analyzed tRNA expression in more than 8000 tumor samples from TCGA, together with their paired mRNA-seq and proteomics data, to determine the Relative Translation Efficiency. We thereby elucidate that the dynamic adaptation of the tRNA pool is largely related to the proliferative state across tissues, which determines tissue-specific translation efficiency. Furthermore, the aberrant translational efficiency of ProCCA and GlyGGT in cancer, among other codons, which is partly regulated by the tRNA gene copy numbers and their promoter DNA methylation, is associated with poor patient survival. Conclusions The distribution of tissue-specific tRNA pools over the whole cellular translatome affects the subsequent translational efficiency, which functionally determines a condition-specific expression program in tissues both in healthy and tumor states.
Pollen Analysis of Natural Bee Honeys from Different Regions of Sri Lanka

Pollen analysis plays an important role when identifying the botanical and geographical origins of bee honey. The aim of the present study was to identify the major plant sources that contribute to the increase of yield of honey which was obtained from selected regions of Sri Lanka such as Ella, Elpitiya, Welimada, Minipe, Loggaloya, Anuradhapura, Kothmale, Haputhale and Nuwara Eliya. The morphology of pollen was observed with light microscope and total pollen counts were expressed in pollen percentage frequency. Based on the analysis, Welimada, Haputhale, Nuwara Eliya and Loggaloya samples were categorized as unifloral honey and remaining honeys were multifloral. Nuwara Eliya, Elpitiya, and Kothmale bee honey samples were categorized as good quality honey because they had absolute pollen count >1,000,000/10g. There were 82 pollen types belonging to 29 families identified through the study. Among different plant families, Myrtaceae, Fabaceae, Asteraceae, Poaceae, and Malvaceae families highly contributed for nectar and pollen sources of honey bee in the areas examined in this study. Through identifying the major plant sources for honey bees, this study demonstrated the potentiality for expanding and sustainable bee keeping practices in Sri Lanka.
Gene editing of BTK using CRISPR/Cas9 to study drug resistance in acute myeloid leukaemia

iii Acknowledgements . iv Table of contents . v List of Figures . ix List of Tables . xii Abbreviations . xiii Chapter 1: Introduction . 1 1.1 Acute myeloid leukaemia . 2 1.1.1 Normal Haematopoiesis . 2 1.1.2 Acute myeloid leukaemia . 4 1.1.3 Pathogenesis and classification of AML . 4 1.1.4 AML Epidemiology . 9 1.1. 5 Treatment and Prognosis for AML . 9 1.2 Protein tyrosine kinases . 10 1.2. 1 TEC protein family of non-receptor tyrosine kinases . 12 1.2. 2 Bruton’s tyrosine kinase (BTK) . 13 1.2. 3 BTK structure and regulation . 14 1.2. 4 The role of BTK in AML . 15 1.3 Ibrutinib . 16 1.3. 1 Targeting protein tyrosine kinases in cancer . 16 1.3. 2 Ibrutinib a BTK inhibitor . 18 1.3. 3 Clinical effects of ibrutinib in B-cell malignancies . 18 1.3. 4 Targeting BTK beyond B-cell malignancies . 20 1.3. 5 Resistance mechanisms for the BTK inhibitor ibrutinib . 21 1.3. 6 Second generation BTK inhibitors . 22 1.4 Genome editing . 23 1.4. 1 Development and mechanism of targeted genome editing . 23
Adaptation and variability of Aedes aegypti in relation to food in the southernmost fringe of its distribution - An interdisciplinary approach

Aedes aegypti is the well-spread main vector of dengue and other viral diseases and in means of mosquito control, it is important to understand adaptation and variability within the species. This study has considered eggs of Ae. aegypti from two close regions in the area of Buenos Aires. The aim was to increase understanding in environmental and genetic characteristics in food intake. From a long-term perspective, this is a contribution to solving the issues of how modelling could take these factors into account, in order to understand or predict adaptive trends and subsequently, permanent modifications in mosquito populations. The experiment was performed in collaboration with the Buenos Aires Mosquito Study Group and was outlined to obtain data of development times and wing lengths of the subpopulations, when exposed to different diets. The subpopulations showed small differences in individuals all the way from egg to adult depending on origin and differences in growth strategies. Hence, assumptions about homogeneity or uniformity within species, that are often made in mosquito control contexts, should be reconsidered. (Less)
Specific Object Recognition and Tracking using Cascade Connection of Different types of CNNs and Time-series filter

Currently, convolutional neural networks (CNN) are widely used for object recognition, and it is common to use already trained network as a basis. However, the retraining cost of CNN to recognize a specific object is expensive in terms of dataset preparation and calculation cost. We propose instead to add a second CNN specialized on the recognition of the desired target. Additionally, a time-series filter is used to stabilize the detection of the target. To confirm the effectiveness of the proposed method, we used outdoor recorded movies and evaluated the accuracy of specific person recognition.
Dual Edge-Triggered D-Type Flip-Flop with Low Power Consumption

In this paper, a novel low-power dual edge-triggered (DET) D-type flip-flop is proposed. This design achieves dual edge-triggered with two parallel data paths work in opposite phases of the clock single. Among them, a latch circuit structure employs differential input data signals which deposits very little capacitance on the clock line is accomplished. For fair comparison, four previously reported DET flipflops along with the proposed DETFF (DET flip-flop) are compared in terms of power consumption and power-delay product (PDP), under different data activities and different data rates. Several HSPICE simulation results show that the proposed DETFF is superior in power reduction at different parameters as compared to the existing DETFFs. Hence, the proposed DETFF is well suited for low power applications.
The Plasmodium falciparum Hsp70-x chaperone assists the heat stress response of the malaria parasite

Plasmodium falciparum is the most lethal of human‐infective malaria parasites. A hallmark of P. falciparum malaria is extensive remodeling of host erythrocytes by the parasite, which facilitates the development of virulence properties such as host cell adhesion to the endothelial lining of the microvasculature. Host remodeling is mediated by a large complement of parasite proteins exported to the erythrocyte; among them is a single heat shock protein (Hsp)70‐class protein chaperone, P. falciparum Hsp70‐x (PfHsp70‐x). PfHsp70‐x was previously shown to assist the development of virulent cytoadherence characteristics. Here, we show that PfHsp70‐x also supports parasite growth under elevated temperature conditions that simulate febrile episodes, especially at the beginning of the parasite life cycle when most of host cell remodeling takes place. Biochemical and biophysical analyses of PfHsp70‐x, including crystallographic structures of its catalytic domain and the J‐domain of its stimulatory Hsp40 cochaperone, suggest that PfHsp70‐x is highly similar to human Hsp70 chaperones endogenous to the erythrocyte. Nevertheless, our results indicate that selective inhibition of PfHsp70‐x function using small molecules may be possible and highlight specific sites of its catalytic domain as potentially of high interest. We discuss the likely roles of PfHsp70‐x and human chaperones in P. falciparum biology and how specific inhibitors may assist us in disentangling their relative contributions. —Day, J., Passecker, A. , Beck, H. ‐P., Vakonakis, I. The Plasmodium falciparum Hsp70‐x chaperone assists the heat stress response of the malaria parasite. FASEB J. 33, 14611‐14624 (2019). www.fasebj. org
Cerberus1 Regulates the Differentiation of Human Embryonic Stem Cells into Definitive Endoderm

Author(s): Zargar, Sahar | Advisor(s): Jhala, Ulupi; Zhang, Dong-Er | Abstract: Cerberus1 is a secreted protein that has emerged as a critical regulator of embryogenesis in mouse, frog, and more recently human embryos. Despite the wealth of information about its roles in embryogenesis, there has yet to be a complete understanding of its role in human embryonic stem cell (hESC) pluripotency and differentiation into cells of the Definitive Endoderm (DE) and eventually insulin-producing, glucose responsive cells. These insulin-producing, glucose responsive cells regulate blood glucose levels and are the focus of regenerative therapies for the treatment of Type 1 Diabetes. Understanding how biochemistry and signal transduction regulate this transition out of pluripotency is not only critical to understand how cells communicate with the extracellular environment but also to develop safe and effective protocols to generate tissues from select cell lines. In this report, we created a model system to modulate DE formation and look at the role of secreted proteins on differentiation. We show that changes in the media from directed differentiation protocols signal the cells, which then actively respond by upregulating secreted proteins such as Cer1. We used conditioned media, Cer1 antibodies, and exogenous Cer1 to show that Cer1 modulates cell fate when it’s secreted by hESCs. Taken together, these results show that Cer1 is not simply a marker of DE but it also plays an active role in regulating differentiation by signaling to the cells that DE formation is complete and therefore halting differentiation. These findings provide insight into how cells communicate with the extracellular aid in enhancement of the production of insulin-secreting, glucose responsive cells across different hESC lines.
Deep Learning of Complex Batch Process Data and Its Application on Quality Prediction

Batch process quality prediction is an important application in manufacturing and chemical industries. The complexity of batch processes is characterized by multiphase, nonlinearity, dynamics, and uneven durations so that modeling of these batch processes is rather difficult. Moreover, there are other challenges in the face of quality prediction. Specifically, the process trajectories over the whole running duration potentially make specific contributions to the final targets so that the prediction issue embraces tremendously high-dimensional inputs but very low-dimensional outputs. This means that the prediction suffers from a severe dimensional imbalance between inputs and outputs. Motivated by these difficulties, this paper proposes a new deep learning-based framework for complex feature representative and quality prediction. Long short-term memory (LSTM) is used to extract comprehensive quality-relevant hidden features from a long-time sequence in each phase, significantly reducing the predictor dimensions. And these features from different phases are further integrated and compressed by a stacked auto-encoder (SAE). A practical industrial example testifies to the efficacy of the proposed framework.
Novel interface for an Online Public Access Catalogue: a citation network approach

The conventional subject search strategy of querying with words and phrases has been creating a lot of difficulties for the users of Online Public Access Catalogue (OPAC) systems because of the matching problems with the system vocabulary. An alternative is to use search by browsing through related records. In the proposed novel interface for the OPAC, a citation network approach is employed for subject access by browsing. [Continues. ]
RECTIFIED ETHANOL PRODUCTION COST ANALYSIS

This paper deals with the impact of the most important factors of the total production costs in bioethanol production. The most influential factors are: total investment costs, price of raw materials (price of biomass, enzymes, yeast), and energy costs. Taking into account these factors, a procedure for estimation total production costs was establish. In order to gain insight into the relationship of production and selling price of bioethanol, price of bioethanol for some countries of the European Union and the United States are given.
A Tailoring of the Unified Architecture Framework's Meta‐Model for the Modeling of Systems‐of‐Systems

Being used by single companies and by coalitions of governments at the same time, Architecture Frameworks have spread widely as a key tool for the enablement of the Model Based Systems Engineering approach. The Unified Architecture Framework, promoted by the Object Management Group, is rapidly emerging as the reference framework to describe Enterprise Architecture, providing a standard representation for both defense and non‐defense organizations’ architecture descriptions. The work described in the present paper concerns the implementation of a simplified meta‐model, derived as a tailoring of the Unified Architecture Framework's full meta‐model, aimed at allowing the usage of the UAF for the description of System Architectures, rather than Enterprise Architectures. The main UAF View Domains concerned with Systems having the characteristics of Systems‐of‐Systems (Operational, Strategic and Resources), will be analyzed and a solution will be shown to allow a simple implementation of SysML models, as an architectural description of such Systems. A study case will also be presented, developed as a joint effort of Leonardo and Aster for the modeling of naval Combat Systems.
L-Arginine protects ovine intestinal epithelial cells from lipopolysaccharide-induced intestinal barrier injury

ABSTRACT This research aims to explore the effect of L-arginine (Arg) on ovine intestinal epithelial cells (IOECs) from lipopolysaccharide (LPS)-induced intestinal barrier injury. IOECs were incubated for 16 h and classified as 4 groups with the replacement of various mediums, including (1) control (Con), Arg-free Dulbecco's modified Eagle's F12 Ham medium (DMEM); (2) Arg treatment, Arg-free DMEM supplemented with 100 μM Arg; (3) LPS treatment, Arg-free DMEM supplemented with 10 μg/mL LPS; (4) LPS with Arg treatment, Arg-free DMEM supplemented with both 10 μg/mL LPS and 100 μM Arg. Arg supplementation to LPS-treated IOECs resulted in lower (P < 0.05) relative Toll-like receptor 4 (TLR4) protein level. Arg supplementation to LPS-treated IOECs resulted in up-regulated (P < 0.05) zonula occludens-1 (ZO-1), peptide transporter 1 (PEPT1) protein levels, and the ratio of phosphorylated mechanistic target of rapamycin (phospho-mTOR)-to-mTOR. The results show that Arg protects IOECs from LPS induced intestinal barrier injury.
Wiring Sympathetic Neuron Subpopulations into Target-Selective Circuits for Homeostasis

The molecular characterization of postganglionic sympathetic neurons by RNA sequencing has allowed the full assessment of gene expression in individual cells and classification of neurons into subpopulations defined by their gene expression profile and developmental history. The identification of growth factor receptor subunits specifically expressed by select neuron subpopulations enabled the demonstration of GDNF family ligands and the respective receptor subunits as instrumental in the innervation of certain targets. These are first critical steps in the attempt to characterize the molecular processes leading to the establishment and maintenance of target-specific sympathetic efferent pathways.
Comparison between the Effect of Feeding Corn Silage or Berseem as a Basal Diet on: 1- Milk Production and Economic Efficiency of Lactating Friesian Cows.

Twelve lactating Friesian cows with the average body weight of 490-560 kg were used in this study. All animals were in the second to fourth lactation season. Cows were randomly distributed into three similar groups (four for each group) to study the effect of the tested rations on milk production and its composition. All groups were individually fed according to NRC (2001) recommendations. The experimental period lasted for 140 days (20 weeks) after calving. The three experimental rations were formulated nearly as follows: (Control): 40 % concentrate feed mixture (CFM) + 32 % rice straw (RS) + 28 % corn silage (S), (Exp.1): 40 % concentrate feed mixture (CFM) + 32 % rice straw (RS) + 28 % berseem (B) and (Exp.2): 40 % concentrate feed mixture (CFM) + 32 % rice straw (RS) + 14 % corn silage (S) + 14 % berseem (B). The average daily milk yield was the highest (p < 0.05) with group fed exp.1 from W1 to W12 compared with the control ration, while there were no significant effect between exp.1 and exp.2 or exp.2 and control ration. The average milk yield were 12.69, 16.05 and 15.17 Kg/day with feeding on control, exp.1 and exp.2 respectively. The milk composition of protein% was higher (p < 0.05) with feeding on exp.2 (2.51%) than feeding on exp.1 (2.29%), but there was no significant effect between exp.1 and control ration (2.37%) or feeding on exp.2 and control ration. The net energy (NEL Mcal/kg milk) values were significantly (p < 0.05) higher with feeding on control or exp.2 (0.64 and 0.63 Mcal/kg milk respectively) than feeding on exp.1 (0.60 Mcal/kg milk). The protein yield and lactose yield (kg/day) were increased (p < 0.05) with feeding on exp.1 and exp.2 rations than feeding on control ration. The highest values of feed conversion (DMI kg/kg FCM) and net energy of the milk (Mcal/kg milk) were with feeding on rations containing corn silage (control) or corn silage with berseem (exp.2) than ration which containing berseem only (exp.1). The highest values (p<0.05) of feed cost were estimated with exp.1 (40.01 LE) and exp.2 (38.07 LE) than feeding on the control diet (36.09 LE), but there was no significant affect between the control and exp.2 or exp.1 and exp.2. With the same trend the profit (LE) values were higher (p<0.05) with feeding an exp.1 (21.63 LE) or feeding with exp.2 (18.69 LE) than feeding with the control (15.35 LE). Corn silage is an important source of digestible effective fibre and can be an economical source of CP in diets for lactating cows, but increased passage rate with feeding berseem which is more digestible forage NDF might increase efficiency of milk production and composition. So feeding on exp.1 or exp.2 resulted in improving milk production, feed conversion and economic efficiency.
A Four-Step Incremental ADC Based on Double Extended Binary Counting With Capacitive DAC

This brief proposes a discrete-time four-step reconfigurable incremental ADC (IADC) which consists of a first-step SAR conversion, a second-step IADC operation, and double extended binary counting (EBC). While coarse conversion with the 8b SAR ADC is preceded, instead of 8b DAC, 7b capacitive DAC based integrator operation in the IADC becomes available to reduce the chip area and power consumption of amplifier. Additional resolution is achieved by performing the EBC twice, where its conversion time is reduced by using the binary operation with a 7b capacitive DAC. The IADC and the EBC are reconfigured to utilize the same sub-blocks of one amplifier and one comparator, thus reducing silicon area and obtaining high linearity. A prototype ADC is fabricated in a 180-nm CMOS process, and it achieves 179.7 dB FoM and consumes 176 $\mu \text{W}$ .
Integrating Program/Project Management and Systems Engineering in Practice

Two practitioners who have experience integrating program/project management and systems engineering conducted two workshops titled ‘Integrating Systems Engineering, Project Management, and Quality Management’ as an INCOSE Enchantment Chapter tutorial and at the 2018 International Symposium (IS18), respectively. The workshops included presentations by the researchers about their organization's integration implementations followed by small group discussion exercises on topics/issues to consider when making integration decisions. Discussion topics were drawn from Rebentisch (Ed., 2017) and included motivations to integrate, organizational environments that support or inhibit integration, influencers and influence, integration metrics, and success and failure contributors. Each exercise concluded with out‐briefs of the small groups' observations, analyses, and recommendations to the collective. A synthesis of these observations, analyses, and recommendations provide the bases for this paper.
A New Design of a Microstrip Antenna with Modified Ground for RFID Applications

A new dual-band monopole microstrip antenna with modified ground structure designed for Radio Frequency Identification (RFID) readers is proposed. The rectangular slots inserted in the ground plan permit to achieve dual frequencies and also provide a broadband operation at high frequency. The entire area of the proposed antenna is 33×35 mm and mounted on an FR4 substrate with dielectric permittivity constant 4.4, thickness of 1.6 mm and loss tangent of 0.025 and fed by a 50 Ohm microstrip line. This antenna has been analyzed and simulated to cover the RFID at 2.45/5.8 GHz. The simulation has been carried out by using two electromagnetic solvers ADS and CST Microwave Studio. By fabricating and measuring the performances of the prototype of the proposed optimal antenna, experimental results show that the dual operating bands excited with -10dB return-loss bandwidths of about 70 MHz centered at 2.45 GHz and of about 490 MHz centered at 5.8 GHz were obtained.