Miracle-dz/UniFAR-FTUs huggingface dataset:
Comparison of gene expression profiles between human erythroid cells derived from fetal liver and adult peripheral blood

Background A key event in human development is the establishment of erythropoietic progenitors in the bone marrow, which is accompanied by a fetal-to-adult switch in hemoglobin expression. Understanding of this event could lead to medical application, notably treatment of sickle cell disease and β-thalassemia. The changes in gene expression of erythropoietic progenitor cells as they migrate from the fetal liver and colonize the bone marrow are still rather poorly understood, as primary fetal liver (FL) tissues are difficult to obtain. Methods We obtained human FL tissue and adult peripheral blood (AB) samples from Thai subjects. Primary CD34+ cells were cultured in vitro in a fetal bovine serum-based culture medium. After 8 days of culture, erythroid cell populations were isolated by flow cytometry. Gene expression in the FL- and AB-derived cells was studied by Affymetrix microarray and reverse-transcription quantitative PCR. The microarray data were combined with that from a previous study of human FL and AB erythroid development, and meta-analysis was performed on the combined dataset. Results FL erythroid cells showed enhanced proliferation and elevated fetal hemoglobin relative to AB cells. A total of 1,391 fetal up-regulated and 329 adult up-regulated genes were identified from microarray data generated in this study. Five hundred ninety-nine fetal up-regulated and 284 adult up-regulated genes with reproducible patterns between this and a previous study were identified by meta-analysis of the combined dataset, which constitute a core set of genes differentially expressed between FL and AB erythroid cells. In addition to these core genes, 826 and 48 novel genes were identified only from data generated in this study to be FL up- and AB up-regulated, respectively. The in vivo relevance for some of these novel genes was demonstrated by pathway analysis, which showed novel genes functioning in pathways known to be important in proliferation and erythropoiesis, including the mitogen-activated protein kinase (MAPK) and the phosphatidyl inositol 3 kinase (PI3K)-Akt pathways. Discussion The genes with upregulated expression in FL cells, which include many novel genes identified from data generated in this study, suggest that cellular proliferation pathways are more active in the fetal stage. Erythroid progenitor cells may thus undergo a reprogramming during ontogenesis in which proliferation is modulated by changes in expression of key regulators, primarily MYC, and others including insulin-like growth factor 2 mRNA-binding protein 3 (IGF2BP3), neuropilin and tolloid-like 2 (NETO2), branched chain amino acid transaminase 1 (BCAT1), tenascin XB (TNXB) and proto-oncogene, AP-1 transcription factor subunit (JUND). This reprogramming may thus be necessary for acquisition of the adult identity and switching of hemoglobin expression.
Spatially Compact MR-Guided Kernel EM for PET Image Reconstruction

Positron emission tomography (PET) is a highly sensitive functional and molecular imaging modality which can measure picomolar concentrations of an injected radionuclide. However, the physical sensitivity of PET is limited, and reducing the injected dose leads to low count data and noisy reconstructed images. A highly effective way of reducing noise is to reparameterize the reconstruction in terms of MR-derived spatial basis functions. Spatial basis functions derived using the kernel method have demonstrated excellent noise reduction properties and maintain shared PET-MR detailed structures. However, as previously shown in the literature, the MR-guided kernel method may lead to excessive smoothing of structures that are only present in the PET data. This paper makes two main contributions in order to address this problem: first, we exploit the potential of the MR-guided kernel method to form more spatially compact basis functions which are able to preserve PET-unique structures, and second, we consider reconstruction at the native MR resolution. The former contribution notably improves the recovery of structures which are unique to the PET data. These adaptations of the kernel method were compared to the conventional implementation of the MR-guided kernel method and also to maximum likelihood expectation maximization, in terms of ability to recover PET unique structures for both simulated and real data. The spatially compact kernel method showed clear visual and quantitative improvements in the reconstruction of the PET unique structures, relative to the conventional kernel method for all sizes of PET unique structures investigated, whilst maintaining to a large extent the impressive noise mitigating and detail preserving properties of the conventional MR-guided kernel method. We therefore conclude that a spatially compact parameterization of the MR-guided kernel method, should be the preferred implementation strategy in order to obviate unnecessary losses in PET-unique details.
Compact Quad-Mode Planar Phased Array With Wideband for 5G Mobile Terminals

In this paper, a quad-mode endfire planar phased antenna array with wide scan angle and 1.2 mm clearance is proposed for 5G mobile terminals. The proposed antenna can obtain over 8 GHz of impedance bandwidth. In this paper, it is suggested to efficiently combine a multimode array element with different radiation patterns for each mode into a phased antenna array. In the array, similar and wide embedded radiation patterns are obtained for the all four modes. Furthermore, a coaxial to differential stripline transition is designed in this paper. The differential feeding structure is very compact and utilizes only MMPX connector and vias. The total scan pattern and coverage efficiency of the measured and simulated phased array antenna are calculated in the range from 25 to 33 GHz, and good agreement between measured and simulated results is observed. The mean coverage efficiency along the frequency range is very similar, but minor difference in variance of coverage efficiency is observed in the measurements. The coverage efficiency of around 50% for the threshold gain of 5 dBi is achieved in the chosen frequency range.
Acute HIIE elicits similar changes in human skeletal muscle mitochondrial H2O2 release, respiration, and cell signaling as endurance exercise even with less work.

It remains unclear whether high-intensity interval exercise (HIIE) elicits distinct molecular responses to traditional endurance exercise relative to the total work performed. We aimed to investigate the influence of exercise intensity on acute perturbations to skeletal muscle mitochondrial function (respiration and reactive oxygen species) and metabolic and redox signaling responses. In a randomized, repeated measures crossover design, eight recreationally active individuals (24 ± 5 yr; V̇o2peak: 48 ± 11 ml·kg-1·min-1) undertook continuous moderate-intensity [CMIE: 30 min, 50% peak power output (PPO)], high-intensity interval (HIIE: 5 × 4 min, 75% PPO, work matched to CMIE), and low-volume sprint interval (SIE: 4 × 30 s) exercise, ≥7 days apart. Each session included muscle biopsies at baseline, immediately, and 3 h postexercise for high-resolution mitochondrial respirometry ( Jo2) and H2O2 emission ( Jh2o2) and gene and protein expression analysis. Immediately postexercise and irrespective of protocol, Jo2 increased during complex I + II leak/state 4 respiration but Jh2o2 decreased ( P < 0.05). AMP-activated protein kinase and acetyl co-A carboxylase phosphorylation increased ~1.5 and 2.5-fold respectively, while thioredoxin-reductase-1 protein abundance was ~35% lower after CMIE vs. SIE ( P < 0.05). At 3 h postexercise, regardless of protocol, Jo2 was lower during both ADP-stimulated state 3 OXPHOS and uncoupled respiration ( P < 0.05) but Jh2o2 trended higher ( P < 0.08) and PPARGC1A mRNA increased ~13-fold, and peroxiredoxin-1 protein decreased ~35%. In conclusion, intermittent exercise performed at high intensities has similar dynamic effects on muscle mitochondrial function compared with endurance exercise, irrespective of whether total workload is matched. This suggests exercise prescription can accommodate individual preferences while generating comparable molecular signals known to promote beneficial metabolic adaptations.
Applications of Variability Analysis Techniques for Continuous Glucose Monitoring Derived Time Series in Diabetic Patients

Methods from non-linear dynamics have enhanced understanding of functional dysregulation in various diseases but received less attention in diabetes. This retrospective cross-sectional study evaluates and compares relationships between indices of non-linear dynamics and traditional glycemic variability, and their potential application in diabetes control. Continuous glucose monitoring provided data for 177 subjects with type 1 (n = 22), type 2 diabetes (n = 143), and 12 non-diabetic subjects. Each time series comprised 576 glucose values. We calculated Poincaré plot measures (SD1, SD2), shape (SFE) and area of the fitting ellipse (AFE), multiscale entropy (MSE) index, and detrended fluctuation exponents (α1, α2). The glycemic variability metrics were the coefficient of variation (%CV) and standard deviation. Time of glucose readings in the target range (TIR) defined the quality of glycemic control. The Poincaré plot indices and α exponents were higher (p < 0.05) in type 1 than in the type 2 diabetes; SD1 (mmol/l): 1.64 ± 0.39 vs. 0.94 ± 0.35, SD2 (mmol/l): 4.06 ± 0.99 vs. 2.12 ± 1.04, AFE (mmol2/l2): 21.71 ± 9.82 vs. 7.25 ± 5.92, and α1: 1.94 ± 0.12 vs. 1.75 ± 0.12, α2: 1.38 ± 0.11 vs. 1.30 ± 0.15. The MSE index decreased consistently from the non-diabetic to the type 1 diabetic group (5.31 ± 1.10 vs. 3.29 ± 0.83, p < 0.001); higher indices correlated with lower %CV values (r = -0.313, p < 0.001). In a subgroup of type 1 diabetes patients, insulin pump therapy significantly decreased SD1 (-0.85 mmol/l), SD2 (-1.90 mmol/l), and AFE (-16.59 mmol2/l2), concomitantly with %CV (-15.60). The MSE index declined from 3.09 ± 0.94 to 1.93 ± 0.40 (p = 0.001), whereas the exponents α1 and α2 did not. On multivariate regression analyses, SD1, SD2, SFE, and AFE emerged as dominant predictors of TIR (β = -0.78, -1.00, -0.29, and -0.58) but %CV as a minor one, though α1 and MSE failed. In the regression models, including SFE, AFE, and α2 (β = -0.32), %CV was not a significant predictor. Poincaré plot descriptors provide additional information to conventional variability metrics and may complement assessment of glycemia, but complexity measures produce mixed results.
Early-season crop mapping using improved artificial immune network (IAIN) and Sentinel data

Substantial efforts have been made to identify crop types by region, but few studies have been able to classify crops in early season, particularly in regions with heterogeneous cropping patterns. This is because image time series with both high spatial and temporal resolution contain a number of irregular time series, which cannot be identified by most existing classifiers. In this study, we firstly proposed an improved artificial immune network (IAIN), and tried to identify major crops in Hengshui, China at early season using IAIN classifier and short image time series. A time series of 15-day composited images was generated from 10 m spatial resolution Sentinel-1 and Sentinel-2 data. Near-infrared (NIR) band and normalized difference vegetation index (NDVI) were selected as optimal bands by pair-wise Jeffries–Matusita distances and Gini importance scores calculated from the random forest algorithm. When using IAIN to identify irregular time series, overall accuracy of winter wheat and summer crops were 99% and 98.55%, respectively. We then used the IAIN classifier and NIR and NDVI time series to identify major crops in the study region. Results showed that winter wheat could be identified 20 days before harvest, as both the producer’s accuracy (PA) and user’s accuracy (UA) values were higher than 95% when an April 1–May 15 time series was used. The PA and UA of cotton and spring maize were higher than 95% with image time series longer than April 1–August 15. As spring maize and cotton mature in late August and September–October, respectively, these two crops can be accurately mapped 4–6 weeks before harvest. In addition, summer maize could be accurately identified after August 15, more than one month before harvest. This study shows the potential of IAIN classifier for dealing with irregular time series and Sentinel-1 and Sentinel-2 image time series at early-season crop type mapping, which is useful for crop management.
Effect of toe joint stiffness and toe shape on walking biomechanics

During typical human walking, the metatarsophalangeal joints undergo extension/flexion, which we term toe joint articulation. This toe joint articulation impacts locomotor performance, as evidenced by prior studies on prostheses, footwear, sports and humanoid robots. However, a knowledge gap exists in our understanding of how individual toe properties (e.g. shape, joint stiffness) affect bipedal locomotion. To address this gap, we designed and built a pair of adjustable foot prostheses that enabled us to independently vary different toe properties, across a broad range of physiological and non-physiological values. We then characterized the effects of varying toe joint stiffness across a range of different ankle joint stiffness conditions, and the effects of varying toe shape on walking biomechanics. Ten able-bodied individuals walked on a treadmill with prostheses mounted bilaterally underneath simulator boots (which immobilized their biological ankles). We collected motion capture and ground reaction force data, then computed joint kinematics and kinetics, and center-of-mass (COM) power and work. To our surprise, we found that varying toe joint stiffness affected COM Push-off dynamics during walking as much as, or in some cases even more than, varying ankle joint stiffness. Increasing toe joint stiffness increased COM Push-off work by up to 48% (6 J), and prosthetic anklefoot Push-off work by up to 181% (12 J). In contrast, large changes in toe shape had little effect on gait. This study brings attention to the toes, an aspect of prosthetic and robotic foot design that is often overlooked or overshadowed by design of the ankle. Optimizing toe joint stiffness in assistive and robotic devices (e.g. prostheses, exoskeletons, robot feet) may provide a complementary means of enhancing Push-off or other aspects of locomotor performance, in conjunction with the more conventional approach of augmenting ankle dynamics. Future studies are needed to isolate the effects of additional toe properties (e.g. toe length).
Childhood Obesity and Firmicutes/Bacteroidetes Ratio in the Gut Microbiota: A Systematic Review.

BACKGROUND The aim of the present study was to undertake a systematic review exploring the relationship between childhood obesity and fecal microorganisms, to answer the following question: "Are Firmicutes and Bacteroidetes a significant risk indicator/factor for obesity in children? " The main search terms were "child" and "obesity" together with "gut microbiota" (PubMed: 2005-2017). The minimal requirements for inclusion were the evaluation of gut microbiota composition and BMI in children between 0 and 13 years of age. METHODS Assessed articles were carefully classified according to a predetermined criterion, and the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) were considered. Seven articles were critically appraised and used as a basis for conclusions. RESULTS Three studies showed a positive association between Bacteroides fragilis and obesity. In addition, a high value of evidence indicated that a decrease in the Bacteroidetes phylum and in Bacteroides/Prevotella groups was related to high BMI. For the Firmicutes phylum, one high-quality study highlighted that it was positively correlated with weight gain. With regard to Firmicutes species, Clostridium leptum, Eubacterium hallii, and Lactobacillus spp. indicated adipose tissue storage, while Clostridium difficile and the Staphylococcus genus were correlated with low BMI. Despite the fact that only one study did not perform real-time polymerase chain reaction to quantify the microorganisms, its results corroborated those of the studies that did. CONCLUSIONS Changes in Firmicutes and Bacteroidetes phyla/species levels might in fact be significant indicators/factors for childhood obesity. However, given the small number of articles appraising these entire phyla and the heterogeneity among the species assessed, further well-designed studies are required to improve the knowledge.
Trust is Good, Control is Better: Creating Secure Clouds by Continuous Auditing

Cloud service certifications (CSC) attempt to assure a high level of security and compliance. However, considering that cloud services are part of an ever-changing environment, multi-year validity periods may put in doubt reliability of such certifications. We argue that continuous auditing (CA) of selected certification criteria is required to assure continuously reliable and secure cloud services, and thereby increase trustworthiness of certifications. CA of cloud services is still in its infancy, thus, we conducted a thorough literature review, interviews, and workshops with practitioners to conceptualize an architecture for continuous cloud service auditing. Our study shows that various criteria should be continuously audited. Yet, we reveal that most of existing methodologies are not applicable for third party auditing purposes. Therefore, we propose a conceptual CA architecture, and highlight important components and processes that have to be implemented. Finally, we discuss benefits and challenges that have to be tackled to diffuse the concept of continuous cloud service auditing. We contribute to knowledge and practice by providing applicable internal and third party auditing methodologies for auditors and providers, linked together in a conceptual architecture. Further on, we provide groundings for future research to implement CA in cloud service contexts.
Generating More Interesting Responses in Neural Conversation Models with Distributional Constraints

Neural conversation models tend to generate safe, generic responses for most inputs. This is due to the limitations of likelihood-based decoding objectives in generation tasks with diverse outputs, such as conversation. To address this challenge, we propose a simple yet effective approach for incorporating side information in the form of distributional constraints over the generated responses. We propose two constraints that help generate more content rich responses that are based on a model of syntax and topics (Griffiths et al., 2005) and semantic similarity (Arora et al., 2016). We evaluate our approach against a variety of competitive baselines, using both automatic metrics and human judgments, showing that our proposed approach generates responses that are much less generic without sacrificing plausibility. A working demo of our code can be found at https://github.com/abaheti95/DC-NeuralConversation.
Control of Sleep Onset by Shal/Kv4 Channels in Drosophila Circadian Neurons

Sleep is highly conserved across animal species. Both wake- and sleep-promoting neurons are implicated in the regulation of wake–sleep transition at dusk in Drosophila. However, little is known about how they cooperate and whether they act via different mechanisms. Here, we demonstrated that in female Drosophila, sleep onset was specifically delayed by blocking the Shaker cognate L channels [Shal; also known as voltage-gated K+ channel 4 (Kv4)] in wake-promoting cells, including large ventral lateral neurons (l-LNvs) and pars intercerebralis (PI), but not in sleep-promoting dorsal neurons (DN1s). Delayed sleep onset was also observed in males by blocking Kv4 activity in wake-promoting neurons. Electrophysiological recordings show that Kv4 channels contribute A-type currents in LNvs and PI cells, but are much less conspicuous in DN1s. Interestingly, blocking Kv4 in wake-promoting neurons preferentially increased firing rates at dusk ∼ZT13, when the resting membrane potentials and firing rates were at lower levels. Furthermore, pigment-dispersing factor (PDF) is essential for the regulation of sleep onset by Kv4 in l-LNvs, and downregulation of PDF receptor (PDFR) in PI neurons advanced sleep onset, indicating Kv4 controls sleep onset via regulating PDF/PDFR signaling in wake-promoting neurons. We propose that Kv4 acts as a sleep onset controller by suppressing membrane excitability in a clock-dependent manner to balance the wake–sleep transition at dusk. Our results have important implications for the understanding and treatment of sleep disorders such as insomnia. SIGNIFICANCE STATEMENT The mechanisms by which our brains reversibly switch from waking to sleep state remain an unanswered and intriguing question in biological research. In this study, we identified that Shal/Kv4, a well known voltage-gated K+ channel, acts as a controller of wake–sleep transition at dusk in Drosophila circadian neurons. We find that interference of Kv4 function with a dominant-negative form (DNKv4) in subsets of circadian neurons specifically disrupts sleep onset at dusk, although Kv4 itself does not exhibit circadian oscillation. Kv4 preferentially downregulates neuronal firings at ZT9–ZT17, supporting that it plays an essential role in wake–sleep transition at dusk. Our findings may help understand and eventually treat sleep disorders such as insomnia.
MKK6 Functions in Two Parallel MAP Kinase Cascades in Immune Signaling1[OPEN]

Arabidopsis MKK6 has multiple functions in plant defense responses in addition to its role in cytokinesis. Arabidopsis (Arabidopsis thaliana) MAP KINASE (MPK) proteins can function in multiple MAP kinase cascades and physiological processes. For instance, MPK4 functions in regulating development as well as in plant defense by participating in two independent MAP kinase cascades: the MEKK1-MKK1/MKK2-MPK4 cascade promotes basal resistance against pathogens and is guarded by the NB-LRR protein SUMM2, whereas the ANPs-MKK6-MPK4 cascade plays an essential role in cytokinesis. Here, we report a novel role for MKK6 in regulating plant immune responses. We found that MKK6 functions similarly to MKK1/MKK2 and works together with MEKK1 and MPK4 to prevent autoactivation of SUMM2-mediated defense responses. Interestingly, loss of MKK6 or ANP2/ANP3 results in constitutive activation of plant defense responses. The autoimmune phenotypes of mkk6 and anp2 anp3 mutant plants can be largely suppressed by a constitutively active mpk4 mutant. Further analysis showed that the constitutive defense response in anp2 anp3 is dependent on the defense regulators PAD4 and EDS1, but not on SUMM2, suggesting that the ANP2/ANP3-MKK6-MPK4 cascade may be guarded by a TIR-NB-LRR protein. Our study shows that MKK6 has multiple functions in plant defense responses in addition to cytokinesis.