Miracle-dz/UniFAR-FTUs huggingface dataset:
Preparations of Small Unilamellar Liposomes

Phospholipids with covalently attached poly(ethylene glycol) (PEG lipids) are commonly used for the preparation of long circulating liposomes. Although it is well known that lipid/PEG-lipid mixed micelles may form above a certain critical concentration of PEG-lipid, little is known about the effects of PEG-lipids on liposome structure and leakage at submicellar concentrations. In this study we have used cryogenic transmission electron microscopy to investigate the effect of PEG(2000)-PE on aggregate structure in preparations of liposomes with different membrane compositions. The results reveal a number of important aggregate structures not documented before. The micrographs show that enclosure of PEG-PE induces the formation of open bilayer discs at concentrations well below those where mixed micelles begin to form. The maximum concentration of PEG-lipid that may be incorporated without alteration of the liposome structure depends on the phospholipid chain length, whereas phospholipid saturation or the presence of cholesterol has little or no effect. The presence of cholesterol does, however, affect the shape of the mixed micelles formed at high concentrations of PEG-lipid. Threadlike micelles form in the absence of cholesterol but adapt a globular shape when cholesterol is present.
Quantitation of Human Whole-Body Synthesis-Secretion Rates of DHA and EPA from Circulating Unesterified α-Linolenic Acid at Steady State

The rate at which dietary α-linolenate (ALA) is desaturated and elongated to its longer chain n-3 PUFA in humans is not agreed upon. In this study, we applied a methodology developed in rodents to investigate whole body, presumably hepatic, synthesis-secretion rates of esterified n-3 PUFA from circulating unesterified ALA in two healthy overweight women after ten weeks of low linoleate diet exposure. During continuous iv infusion of d5-ALA, 17 arterial blood samples were collected from each subject at −10, 0, 10, 20, 40, 60, 80, 100, 120, 150, 180, 210 min, and at 4, 5, 6, 7, and 8 h after beginning infusion. Plasma esterified d5-n-3 PUFA concentrations were plotted against infusion time and fit to a sigmoidal curve using nonlinear regression. These curves were used to estimate kinetic parameters using a kinetic analysis developed in rodents. Calculated synthesis-secretion rates of esterified eicosapentaenoate (EPA), n-3 docosapentaenoate, docosahexaenoic acid (DHA), tetracosapentaenate, and tetracosahexaenoate from circulating Corresponding author: CAPT Joseph R. Hibbeln, MD, SNN/LMBB, NIAAA, NIH, Bethesda, MD 20892, USA, Tel: 301-594-3034, Fax: 301-594-0035, jhibbeln@mail.nih. gov. Conflict of Interest: Authors declare no conflict of interest. Authors’ contributions are as follows (in the alphabetic order): Clinical trial design, research, and PIs: CER, JRH Designed and conducted research: ABC, BVM, CER, CTC, JRH, NMS, RPB, SFM, SIR, YHL Provided essential iv infusion material: HKJ Data analysis and interpretation: AFD, CTC, RPB, SIR, YHL Wrote paper: AFD, JRH, RPB, SIR, YHL Revised manuscript: CER, SFM HHS Public Access Author manuscript Lipids. Author manuscript; available in PMC 2019 August 03. Published in final edited form as: Lipids. 2018 May ; 53(5): 547–558. doi:10.1002/lipd.12055. A uhor M anscript
Oriented Membrane System

The conformation of uniformly 13C-labeled sulfoquinovosyldiacylglycerol (SQDG) is studied in both membrane and solution environments using NMR spectroscopy. Analysis in a membrane-like environment is based on the measurement of dipolar interactions between 13C_13C and 1H-13C spin pairs and on the measurement of 13C chemical shift anisotropy offsets, which appear in magnetically oriented phospholipid-based membrane fragments. Potential energy maps for glycosidic torsions, 4, i/, and 01, are calculated with a membrane interaction energy and are used in the interpretation of experimental data. The membrane-bound description for SQDG is most consistent with a set of low-energy conformations that extends the headgroup of SQDG away from the membrane surface. Analysis of the conformation of SQDG in CD30D solution is based on measured 3JCH scalar couplings. The description of the solution conformation is modeled as a mixture of low-energy conformers predicted in the absence of a membrane interaction term and involves more extensive motional averaging than the model for SQDG embedded in the lipid matrix.
Higher Fludarabine and Cyclophosphamide Exposures Lead to Worse Outcomes in Reduced-Intensity Conditioning Hematopoietic Cell Transplantation for Adult Hematologic Malignancy

Reduced-intensity conditioning regimens using fludarabine (Flu) and cyclophosphamide (Cy) have been widely used in hematopoietic cell transplantation (HCT) recipients. The optimal exposure of these agents remains to be determined. We aimed to delineate the exposure-outcome associations of Flu and Cy separately and then both combined on HCT outcomes. This is a single-center, observational, pharmacokinetic (PK)-pharmacodynamic (PD) study of Flu and Cy in HCT recipients age ≥18 years who received Cy (50 mg/kg in a single dose), Flu (150 to 200 mg/m2 given as 5 daily doses), and total body irradiation (TBI; 200 cGy). We measured trough concentrations of 9-β-D-arabinosyl-2-fluorade-nine (F-ara-A), an active metabolite of Flu, on days −5 and −4 (F-ara-ADay-5 and F-ara-ADay-4, respectively), and measured phosphoramide mustard (PM), the final active metabolite of Cy, and estimated the area under the curve (AUC). The 89 enrolled patients had a nonrelapse mortality (NRM) of 9% (95% confidence interval [CI], 3% to 15%) at day +100 and 15% (95% CI, 7% to 22%) at day +180, and an overall survival (OS) Correspondence and reprint requests: Pamala A. Jacobson, Department of Experimental and Clinical Pharmacology, University of Minnesota College of Pharmacy, MN, 7-115 Weaver-Densford Hall, 308 Harvard St SE, Minneapolis, MN 55455. jacob117@umn.edu (P.A. Jacobson). Conflict of interest statement: C.B. has received research funding from Nant, Fate Therapeutics, and GamidaCell and has served as a consultant for AlloVir (Data Safety and Monitoring Board) and BlueRock Bio. SUPPLEMENTARY MATERIALS Supplementary material associated with this article can be found in the online version at doi:10.1016/j.jtct. 2021.05. 013. HHS Public Access Author manuscript Transplant Cell Ther. Author manuscript; available in PMC 2021 November 28. Published in final edited form as: Transplant Cell Ther. 2021 September ; 27(9): 773.e1–773.e8. doi:10.1016/j.jtct. 2021.05. 013. A uhor M anscript
A simple and cost-effective method for producing small interfering RNAs with high ef®cacy

Small interfering RNAs (siRNAs) are powerful RNA interference (RNAi) reagents for directed posttranscriptional gene silencing. Exogenous siRNA is frequently used in RNAi studies. However, due to profound differences in the activity of siRNAs targeted to different regions of a gene, several reagents may have to be screened for optimal activity. This approach is expensive due to the cost of chemical synthesis of RNAs. We report a technically simple, quick and cost-effective method for the production of siRNAs that makes use of in vitro transcription and deoxyribozyme digestion of the transcripts to produce the desired sequence and length. The method allows for several siRNAs to be produced in parallel at much reduced costs. The siRNAs produced with this method were tested in MDA-MB-231 human breast cancer cells for ef®cacy against the type 1 insulin-like growth factor receptor (IGF1R) mRNA and they caused dose-dependent inhibition of IGF1R expression comparable to that induced by chemically synthesised siRNAs of the same sequence. This method is also useful for producing long RNA fragments of de®ned length and sequence that may be dif®cult to synthesise chemically, and also for producing large quantities of RNAs for applications including structural studies and the study of interactions between RNA and other molecules, such as proteins, other nucleic
Chromosome 11pi, in Congenital Lactic Acidosis

We have identified and sequenced a cDNA that encodes an apparent human orthologue of a yeast protein-X component (ScPDX1) of pyruvate dehydrogenase multienzyme complexes. The new human cDNA that has been referred to as "HsPDX1 " cDNA was cloned by use of the "database cloning" strategy and had a 1,506-bp open reading frame. The amino acid sequence of the protein encoded by the cDNA was 20% identical with that encoded by the yeast PDX1 gene and 40% identical with that encoded by the lipoate acetyltransferase component of the pyruvate dehydrogenase and included a lipoyl-bearing domain that is conserved in some dehydrogenase enzyme complexes. Northern blot analysis demonstrated that the major HsPDX1 mRNA was 2.5 kb in length and was expressed mainly in human skeletal and cardiac muscles but was also present, at low levels, in other tissues. FISH analysis performed with a Pt-derived artifical chromosome (PAC)-containing HsPDX1 gene sublocalized the gene to 11pl.3. Molecular investigation of PDX1 deficiency in four patients with neonatal lactic acidemias revealed mutations 78de185 and 965de159 in a homozygous state, and one other patient had no PDX1 mRNA expression.
Sequence analysis Simulation, power evaluation and sample size recommendation for single-cell RNA-seq

Motivation: Determining the sample size for adequate power to detect statistical signiﬁcance is a crucial step at the design stage for high-throughput experiments. Even though a number of methods and tools are available for sample size calculation for microarray and RNA-seq in the context of differential expression (DE), this topic in the ﬁeld of single-cell RNA sequencing is understudied. Moreover, the unique data characteristics present in scRNA-seq such as sparsity and heterogeneity increase the challenge. Results: We propose POWSC, a simulation-based method, to provide power evaluation and sample size recommendation for single-cell RNA-sequencing DE analysis. POWSC consists of a data simulator that creates realistic expression data, and a power assessor that provides a comprehensive evaluation and visualization of the power and sample size relationship. The data simulator in POWSC outperforms two other state-of-art simulators in capturing key characteristics of real datasets. The power assessor in POWSC provides a variety of power evaluations including stratiﬁed and marginal power analyses for DEs characterized by two forms (phase transition or magnitude tuning), under different comparison scenarios. In addition, POWSC offers information for optimizing the tradeoffs between sample size and sequencing depth with the same total reads. Availability and implementation: POWSC is an open-source R package available online at https://github.com/ suke18/POWSC.
A Novel Intra-Oral Diabetes Screening Approach in Periodontal Patients: Results of a Pilot Study

Background—This pilot study examined whether a novel diabetes screening approach using gingival crevicular blood (GCB) could be used to test for hemoglobin A1c (HbA1c) during the periodontal visit. Methods—At a large periodontics clinic, finger stick blood (FSB) samples from 120 patients as well as GCB samples from those patients with adequate bleeding on probing were collected on special blood collection cards and were analyzed for HbA1c levels in a laboratory. The Pearson correlation coefficient was used to measure correlation between FSB and GCB HbA1c values for 75 paired FSB and GCB samples. A Receiver Operator Characteristic Curve (ROC) analysis was performed to determine an optimal GCB HbA1c criterion value for a positive diabetes screen. Results—For the 75 paired samples, the Pearson correlation coefficient was . 842. The ROC analysis identified a criterion value of 6.3% for the GCB HbA1c test with high sensitivity (.933) and high specificity (.900) corresponding to FSB HbA1c values of 6.5% or greater (in the diabetes range). Using this GCB HbA1c criterion value for 27 additional paired samples in which there was an unidentified component observed to co-elute within the elution window of GCB HbA1c in the laboratory, there was agreement between FSB and GCB values for 24 of the pairs according to whether they were both within, or both outside of the diabetes range. Conclusions—Using a criterion value of 6.3%, GCB samples are acceptable for HbA1c testing to screen for diabetes in most persons with bleeding on probing at the GCB collection site.
The lifetime of charged dust in the atmosphere

Abstract Wind-blown dust plays a critical role in numerous geophysical and biological systems, yet current models fail to explain the transport of coarse-mode particles (>5 μm) to great distances from their sources. For particles larger than a few microns, electrostatic effects have been invoked to account for longer-than-predicted atmospheric residence times. Although much effort has focused on elucidating the charging processes, comparatively little effort has been expended understanding the stability of charge on particles once electrified. Overall, electrostatic-driven transport requires that charge remain present on particles for days to weeks. Here, we present a set of experiments designed to explore the longevity of electrostatic charge on levitated airborne particles after a single charging event. Using an acoustic levitator, we measured the charge on particles of different material compositions suspended in atmospheric conditions for long periods of time. In dry environments, the total charge on particles decayed in over 1 week. The decay timescale decreased to days in humid environments. These results were independent of particle material and charge polarity. However, exposure to UV radiation could both increase and decrease the decay time depending on polarity. Our work suggests that the rate of charge decay on airborne particles is solely determined by ion capture from the air. Furthermore, using a one-dimensional sedimentation model, we predict that atmospheric dust of order 10 μm will experience the largest change in residence time due to electrostatic forces.
A Massive, Dusty, Hi Absorption–Selected Galaxy at z ≈ 2.46 Identified in a CO Emission Survey

We report a NOrthern Extended Millimeter Array (NOEMA) and Atacama Large Millimeter/submillimeter Array search for redshifted CO emission from the galaxies associated with seven high-metallicity ([M/H] ≥ −1.03) damped Lyα absorbers (DLAs) at z ≈ 1.64–2.51. Our observations yielded one new detection of CO(3–2) emission from a galaxy at z = 2.4604 using NOEMA, associated with the z = 2.4628 DLA toward QSO B0201+365. Including previous searches, our search results in detection rates of CO emission of ≈56−24+38 % and ≈11−9+26 %, respectively, in the fields of DLAs with [M/H] > −0.3 and [M/H] < −0.3. Further, the Hi–selected galaxies associated with five DLAs with [M/H] > −0.3 all have high molecular gas masses, ≳5 × 1010 M ⊙. This indicates that the highest-metallicity DLAs at z ≈ 2 are associated with the most massive galaxies. The newly identified z ≈ 2.4604 Hi–selected galaxy, DLA0201+365g, has an impact parameter of ≈7 kpc to the QSO sightline, and an implied molecular gas mass of (5.04 ± 0.78) × 1010 × (α CO/4.36) × (r 31/0.55) M ⊙. Archival Hubble Space Telescope Wide Field and Planetary Camera 2 imaging covering the rest-frame near-ultraviolet (NUV) and far-ultraviolet (FUV) emission from this galaxy yield nondetections of rest-frame NUV and FUV emission, and a 5σ upper limit of 2.3 M ⊙ yr−1 on the unobscured star formation rate (SFR). The low NUV-based SFR estimate, despite the very high molecular gas mass, indicates that DLA0201+365g either is a very dusty galaxy, or has a molecular gas depletion time that is around 2 orders of magnitude larger than that of star-forming galaxies at similar redshifts.
A High Resolution Multi-exposure Stereoscopic Image & Video Database of Natural Scenes

—Immersive displays such as VR headsets, AR glasses, Multiview displays, Free point televisions have emerged as a new class of display technologies in recent years, offering a better visual experience and viewer engagement as compared to conventional displays. With the evolution of 3D video and display technologies, the consumer market for High Dynamic Range (HDR) cameras and displays is quickly growing. The lack of appropriate experimental data is a critical hindrance for the development of primary research efforts in the ﬁeld of 3D HDR video technology. Also, the unavailability of sufﬁcient real-world multi-exposure experimental dataset is a major bottleneck for HDR imaging research, thereby limiting the quality of experience (QoE) for the viewers. In this paper, we introduce a diversiﬁed stereoscopic multi-exposure dataset captured within the campus of Indian Institute of Technology Madras, which is home to a diverse ﬂora and fauna. The dataset is captured using ZED stereoscopic camera and provides intricate scenes of outdoor locations such as gardens, roadside views, festival venues, buildings and indoor locations such as academic and residential areas. The proposed dataset accommodates wide depth range, complex depth structure, complicate object movement, illumination variations, rich color dynamics, texture discrepancy in addition to signiﬁcant randomness introduced by moving camera and background motion. The proposed dataset is made publicly available to the research community. Furthermore, the procedure for capturing, aligning and calibrating multi-exposure stereo videos and images is described in detail. Finally, we have discussed the progress, challenges, potential use cases and future research opportunities with respect to HDR imaging, depth estimation, consistent tone mapping and 3D HDR coding.
A new life for sterile neutrino dark matter after the pandemic

We propose a novel mechanism to generate sterile neutrinos $\nu_s$ in the early Universe, by converting ordinary neutrinos $\nu_\alpha$ in scattering processes $\nu_s\nu_\alpha\to\nu_s\nu_s$. After initial production by oscillations, this leads to an exponential growth in the $\nu_s$ abundance. We show that such a production regime naturally occurs for self-interacting $\nu_s$, and that this opens up significant new parameter space where $\nu_s$ make up all of the observed dark matter. Our results provide strong motivation to further push the sensitivity of X-ray line searches, and to improve on constraints from structure formation.
On the Maximum Hessian Eigenvalue and Generalization

The mechanisms by which certain training interventions, such as increasing learning rates and applying batch normalization, improve the generalization of deep networks remains a mystery. Prior works have speculated that"flatter"solutions generalize better than"sharper"solutions to unseen data, motivating several metrics for measuring flatness (particularly $\lambda_{max}$, the largest eigenvalue of the Hessian of the loss); and algorithms, such as Sharpness-Aware Minimization (SAM) [1], that directly optimize for flatness. Other works question the link between $\lambda_{max}$ and generalization. In this paper, we present findings that call $\lambda_{max}$'s influence on generalization further into question. We show that: (1) while larger learning rates reduce $\lambda_{max}$ for all batch sizes, generalization benefits sometimes vanish at larger batch sizes; (2) by scaling batch size and learning rate simultaneously, we can change $\lambda_{max}$ without affecting generalization; (3) while SAM produces smaller $\lambda_{max}$ for all batch sizes, generalization benefits (also) vanish with larger batch sizes; (4) for dropout, excessively high dropout probabilities can degrade generalization, even as they promote smaller $\lambda_{max}$; and (5) while batch-normalization does not consistently produce smaller $\lambda_{max}$, it nevertheless confers generalization benefits. While our experiments affirm the generalization benefits of large learning rates and SAM for minibatch SGD, the GD-SGD discrepancy demonstrates limits to $\lambda_{max}$'s ability to explain generalization in neural networks.
Evaluation of Embedding Models for Automatic Extraction and Classification of Acknowledged Entities in Scientific Documents (short paper)

Acknowledgments in scientific papers may give an insight into aspects of the scientific community, such as reward systems, collaboration patterns, and hidden research trends. The aim of the paper is to evaluate the performance of different embedding models for the task of automatic extraction and classification of acknowledged entities from the acknowledgment text in scientific papers. We trained and implemented a named entity recognition (NER) task using the Flair NLP-framework. The training was conducted using three default Flair NER models with two differently-sized corpora. The Flair Embeddings model trained on the larger training corpus showed the best accuracy of 0.77. Our model is able to recognize six entity types: funding agency, grant number, individuals, university, corporation and miscellaneous. The model works more precise for some entity types than the others, thus, individuals and grant numbers showed very good F1-Score over 0.9. Most of the previous works on acknowledgement analysis were limited by the manual evaluation of data and therefore by the amount of processed data. This model can be applied for the comprehensive analysis of the acknowledgement texts and may potentially make a great contribution to the field of automated acknowledgement analysis.
Recognising Affordances in Predicted Futures to Plan With Consideration of Non-Canonical Affordance Effects

We propose a novel system for action sequence planning based on a combination of affordance recognition and a neural forward model predicting the effects of affordance execution. By performing affordance recognition on predicted futures, we avoid reliance on explicit affordance effect definitions for multi-step planning. Because the system learns affordance effects from experience data, the system can foresee not just the canonical effects of an affordance, but also situation-specific side-effects. This allows the system to avoid planning failures due to such non-canonical effects, and makes it possible to exploit non-canonical effects for realising a given goal. We evaluate the system in simulation, on a set of test tasks that require consideration of canonical and non-canonical affordance effects.
Sensor Observability Index: Evaluating Sensor Alignment for Task-Space Observability in Robotic Manipulators

In this paper, we propose a preliminary definition and analysis of the novel concept of sensor observability index. The goal is to analyse and evaluate the performance of distributed directional or axial-based sensors to observe specific axes in task space as a function of joint configuration in serial robot manipulators. For example, joint torque sensors are often used in serial robot manipulators and assumed to be perfectly capable of estimating end effector forces, but certain joint configurations may cause one or more task-space axes to be unobservable as a result of how the joint torque sensors are aligned. The proposed sensor observability provides a method to analyse the quality of the current robot configuration to observe the task space. Parallels are drawn between sensor observability and the traditional kinematic Jacobian for the particular case of joint torque sensors in serial robot manipulators. Although similar information can be retrieved from kinematic analysis of the Jacobian transpose in serial manipulators, sensor observability is shown to be more generalizable in terms of analysing non-joint-mounted sensors and other sensor types. In addition, null-space analysis of the Jacobian transpose is susceptible to false observability singularities. Simulations and experiments using the robot Baxter demonstrate the importance of maintaining proper sensor observability in physical interactions.