snu-aidas/HVMap-dataset huggingface dataset:
Mitotic chromosomes fold by condensin-dependent helical winding of chromatin loop arrays

During mitosis, chromosomes fold into compacted rod shaped structures. We combined imaging and Hi-C of synchronous DT40 cell cultures with polymer simulations to determine how interphase chromosomes are converted into compressed arrays of loops characteristic of mitotic chromosomes. We found that the interphase organization is disassembled within minutes of prophase entry and by late prophase chromosomes are already folded as arrays of consecutive loops. During prometaphase, this array reorganizes to form a helical arrangement of nested loops. Polymer simulations reveal that Hi-C data are inconsistent with solenoidal coiling of the entire chromatid, but instead suggest a centrally located helically twisted axis from which consecutive loops emanate as in a spiral staircase. Chromosomes subsequently shorten through progressive helical winding, with the numbers of loops per turn increasing so that the size of a helical turn grows from around 3 Mb (~40 loops) to ~12 Mb (~150 loops) in fully condensed metaphase chromosomes. Condensin is essential to disassemble the interphase chromatin conformation. Analysis of mutants revealed differing roles for condensin I and II during these processes. Either condensin can mediate formation of loop arrays. However, condensin II was required for helical winding during prometaphase, whereas condensin I modulated the size and arrangement of loops inside the helical turns. These observations identify a mitotic chromosome morphogenesis pathway in which folding of linear loop arrays produces long thin chromosomes during prophase that then shorten by progressive growth of loops and helical winding during prometaphase.
REVIEW ON CLINICALLY DEVELOPING ANTIBIOTICS

The world is running out of antibiotics. Between 1940 and 1962, more than 20 new classes of antibiotics were marketed. Since then, only two new classes of antibiotics were marketed. Now, not enough analogues are reaching the market to stem the tide of antibiotic resistance, particularly among gram-negative bacteria which indicates the need of novel antibiotics for their effective action. This review describes those antibiotics in late-stage clinical development. Most of them belong to existing antibiotic classes and a few with a narrow spectrum of activity are novel compounds directed against novel targets. The reasons for some of the past failures to find new molecules and a path forward to help attract investments to fund the discovery of new antibiotics are described.
Improved Au/Zn/Au ohmic contacts for p-type InP

In this work, an innovated Si3N4 as an out-diffusion barrier layer to Au/Zn/Au contact system for p-type InP has been proposed. Before the contacts were annealed, Si3N4 layer was deposited on the Au(200Å)/Zn(700Å)/Au(200Å), then the Si3N4 was removed by HF and a 2000A layer of pure gold was deposited to facilitate wire bonding. The specific contact resistance dropped to a minimum value of 6×10-7 Ω • cm2 (for an acceptor concentration of about 3×1018 cm-3) and the contact became perfectly Ohmic. Besides, Si3N4 layer is an excellent passivation layer and antireflection coating in InP/InGaAs/InP (p-i-n) photodiodes.
The reclamation of brine generated from desalination process by bipolar membrane electrodialysis

Abstract Some techno-economical analyses and environmental impact evaluation have proved that bipolar membrane electrodialysis (BMED) is feasible for the reclamation of industrial saline water. However, to date, the technology cannot be put into practice due to some unsolved application-oriented problems, such as the requirements of BMED for feed solution, the availability of the produced acid and base, relatively high salt concentration of the effluent, and relatively low desalinating efficiency and capacity. In this work, a novel hybrid process, which coupled conventional electrodialysis installed with monovalent selective cation-exchange membranes with BMED running in a constant-voltage mode, was designed to reclaim brine generated from surface water desalination by the ion-exchange process. Subsequently, the response surface methodology was employed to establish the empirical models for understanding the influences of some initial operating conditions on BMED performance. Finally, the BMED-based reclamation scheme was confirmed again by a continuous BMED experiment on real solution. Specially, the effects of product concentration on current efficiency and energy consumption were investigated. In this case, an acceptable current efficiency and energy consumption were obtained on the basis of the conventional membranes and spacers when the product concentration was set as 0.9 M, which is adequate for the regeneration of ion-exchange resins.
Process analysis and economic evaluation for Poly(3-hydroxybutyrate) production by fermentation

Abstract Several processes for the production and recovery of poly(3-hydroxybutyrate) (PHB) by Alcaligenes eutrophus, Alcaligenes latus, Methylobacterium organophilum, and recombinant Escherichia coli were designed based on the previously reported data and analyzed by computer-aided bioprocess design. PHB productivity, content, and yield significantly affected the final price of PHB. For the annual production of 2,850 tonnes of purified PHB, the process employing A. eutrophus with the recovery method of surfactant-hypochlorite digestion resulted in lowest price of PHB, $ 5.58/kg. As the production scale increased to one million tonnes per year, the price of PHB dropped to $ 4.75/kg. The cost of carbon substrate significantly affected the overall economics in large production scale. Therefore, the production cost can be considerably lowered when agricultural wastes, such as whey and molasses, are used.
Modification in the chemical bath deposition apparatus, growth and characterization of CdS semiconducting thin films for photovoltaic applications

Abstract In this paper, growth and characterization of CdS thin films by Chemical Bath Deposition (CBD) technique using the reaction between CdCl 2 , (NH 2 ) 2 CS and NH 3 in an aqueous solution has been reported. The parameters actively involved in the process of deposition have been identified. A commonly available CBD system has been sucessfully modified to obtain the precious control over the pH of the solution at 90°C during the deposition and studies have been made to understand the fundamental parameters like concentrations of the solution, pH and temperature of the solution involved in the chemical bath deposition of CdS. It is confirmed that the pH of the solution plays a vital role in the quality of the CBD–CdS films. Structural, optical and electrical properties have been analysed for the as-deposited and annealed films. XRD studies on the CBD–CdS films reveal that the change in Cadmium ion concentration in the bath results in the change in crystallization from cubic phase with (1 1 1) predominant orientation to a hexagonal phase with (0 0 2) predominant orientation. The structural changes due to varying cadmium ion concentration in the bath affects the optical and electrical properties. Optimum electrical resistivity, band gap and refractive index value are observed for the annealed films deposited from 0.8 M cadmium ion concentration. The films are suitable for solar cell fabrication. Further on, annealing the samples at 350°C in H 2 for 30 min resulted in an increased diffraction intensity as well as shifts in the peak towards lower scattering angles due to enlarged CdS unit cell. This in turn brought about an increase in the lattice parameters and narrowing in the band-gap values. The results are compared with the analysis of previous work.
Combined sampler robot and high-performance liquid chromatography: a fully automated system for biological small-angle X-ray scattering experiments at the Synchrotron SOLEIL SWING beamline

Small-angle X-ray scattering for macromolecules in solution is now widely used in structural biology to complement high-resolution structure determination obtained by X-ray crystallography or NMR. In the context of third-generation synchrotron sources, this increasing interest leads to developments in sample environments and automation. The presence of an online purification system is justified by the need for sample monodispersity. A combined system including an auto-sampler robot and online high-performance liquid chromatography (HPLC) has been developed and optimized at the SWING beamline of Synchrotron SOLEIL (Gif-sur-Yvette, France). In the sample changer mode, a few microlitres of sample can be injected between two air bubbles and circulated at a controlled speed of typically 40 µl min−1. A maximum of 14 samples per hour could be measured in this mode by remote controlling the sample injections. In the HPLC mode, an initially polydisperse sample can be separated into each of its components before immediate data acquisition. The sample cell is thermostated, and offers a visualization control and online UV–Vis absorption monitoring.
Feasibility assessment of desalination application in Australian traditional agriculture

Abstract Within some data limitations, the paper provides a first assessment of areas in Australia with potential for implementing desalination technologies to supply agricultural water. At the national scale, these areas were identified based on a set of selected criteria: distance from land currently used for irrigated agriculture and feedlots; distance from town sites; exclusion of areas of environmental protection; exclusion of areas with surface elevation greater than 600 m AHD; and exclusion of regions with limited groundwater resources. Industries involved in the production of high-value crops are most likely to benefit from desalinated water as they use more-efficient irrigation practices and have the highest gross value of irrigated agricultural production. Groundwater was identified as the most likely feedwater source for cost-effective desalination, which is also the case worldwide. Brine disposal is a major factor in overall cost effectiveness of desalination. When feedwater salinity is relatively low, mixing permeate with feedwater leads to an increase in water production and a reduction in water cost. It was estimated that Australian farmers are unlikely to pay more than AU$1.2/kL for agricultural water. Generally for agriculture, desalinated water is still more expensive than water from other sources; however, there are likely to be circumstances when the costs could be comparable.
Development of a specific monoclonal antibody assay and a rapid testing strip for the detection of apramycin residues in food samples

ABSTRACTA specific monoclonal antibody (MAb) against apramycin (AP) was produced and used to develop an indirect competitive enzyme-linked immunosorbent assay (idcELISA) and a rapid testing strip for the detection of AP residues in foods. MAb exhibited negligible cross-reactivity with other aminoglycosides. Under optimized conditions in 0.01 M PBS, the half maximum inhibitory concentration (IC50) of MAb was 0.41 ng/ml with a limit of detection (LOD) of 0.15 ng/ml. The ELISA results were obtained within 90 min. The mean recoveries from all the spiked food samples were within the range of 79.02–105.49%, with coefficients of variation in the range of 2.21–11.4%. The strip test results obtained within 5 min had visual LODs in the range 2.5–5 µg/kg (ng/ml) for all food samples tested. Therefore, the developed strip test represents a fast and convenient detection method of AP residues in foods.
Utilization of Desalination Brine for Sodium Hydroxide Production: Technologies, Engineering Principles, Recovery Limits, and Future Directions

As global desalination capacity continues its rapid growth, the impetus for reducing the adverse environmental impacts of brine discharge grows concurrently. Although modern brine outfall designs have significantly limited such impacts, they are costly. Recovering valuable components and chemical derivatives from brine has potential to resolve both environmental and economic concerns. In this article, methods for producing sodium hydroxide (“caustic”) from seawater reverse osmosis (SWRO) brine for internal reuse, which typically involve brine purification, brine concentration, and sodium chloride electrolysis, are reviewed. Because process energy consumption drives process cost and caustic purity determines product usability in drinking water systems, reviewed technologies are benchmarked against thermodynamic minimum energy consumption and maximum (stoichiometric) NaOH production rates. After individual reviews of brine purification, concentration, and electrolysis technologies, five existing facilities ...
Coming soon to a Wal-Mart near you

According to the Web site of the Association for Automatic Identification and Data Capture Technologies [http://www.aimglobal.org/technologies/rfid], "radio frequency identification (RFID) technology is an automatic way to collect product, place, and time or transaction data quickly and easily without human intervention or error. " With the ability to track everything from crates of disposable razors to individual peanut-butter jars on the store shelves, RFID technology offers the potential of "real-time supply chain visibility. " Promoters of RFID technology feel [C. Humer, 2003] that "RF tags are to this decade what the Internet was to the 1990's-a promise of radical change in the way business is done. " However, before the full potential of RFID technology can be realized, several hurdles need to be overcome: reliability, cost, lack of standards, and security. As these hurdles gradually diminish, Wal-Mart publicly embraces the technology.
Innovative beneficial reuse of reverse osmosis concentrate using bipolar membrane electrodialysis and electrochlorination processes

Reverse osmosis (RO) is a widely used and rapidly growing desalination technology. A major disadvantage of this process is that the concentrate from the RO process, which could be as much as 25% of the feed stream, represents a polluting stream. This waste stream could pose a significant challenge to the implementation of this process, particularly for inland communities which do not have the option of ocean disposal. An excellent environmentally benign approach to disposal could be beneficial reuse of the waste stream. This study presents two innovative beneficial reuse strategies for RO concentrate produced by an integrated membrane system (IMS) from a wastewater reclamation facility. The technologies evaluated in this study included bipolar membrane electrodialysis (BMED) for conversion of RO concentrate into mixed acid and mixed base streams, and electrochlorination (EC) for onsite chlorine generation. Bench-scale studies conducted with BMED demonstrated that RO concentrate could be desalted while producing mixed acids and mixed bases with concentrations as high as 0.2N. Similarly, the EC process was capable of producing a 0.6% hypochlorite solution from RO concentrate. The acids and bases as well as the hypochlorite produced could be directly applied to the RO process as well as upstream pre-treatment processes. A preliminary economic evaluation of the viability of these two approaches was conducted by conducting rough order of magnitude cost estimates based on the bench-scale performance of these processes on RO concentrate. A comparison of the overall costs of an Integrated Membrane System utilizing these innovative reuse strategies with conventional disposal options and thermal zero liquid discharge treatment is presented. This comparison indicates that a reuse approach might be economically viable for inland wastewater reuse facilities that utilize RO membranes and have limited options for concentrate disposal.
Amplification of siRNA in Caenorhabditis elegans generates a transgenerational sequence-targeted histone H3 lysine 9 methylation footprint

Exogenous double-stranded RNA (dsRNA) has been shown to exert homology-dependent effects at the level of both target mRNA stability and chromatin structure. Using C. elegans undergoing RNAi as an animal model, we have investigated the generality, scope and longevity of dsRNA-targeted chromatin effects and their dependence on components of the RNAi machinery. Using high-resolution genome-wide chromatin profiling, we found that a diverse set of genes can be induced to acquire locus-specific enrichment of histone H3 lysine 9 trimethylation (H3K9me3), with modification footprints extending several kilobases from the site of dsRNA homology and with locus specificity sufficient to distinguish the targeted locus from the other 20,000 genes in the C. elegans genome. Genetic analysis of the response indicated that factors responsible for secondary siRNA production during RNAi were required for effective targeting of chromatin. Temporal analysis revealed that H3K9me3, once triggered by dsRNA, can be maintained in the absence of dsRNA for at least two generations before being lost. These results implicate dsRNA-triggered chromatin modification in C. elegans as a programmable and locus-specific response defining a metastable state that can persist through generational boundaries.
Physicians' initial management of acute low back pain versus evidence-based guidelines. Influence of sciatica.

BACKGROUND Little information is available on physician characteristics and patient presentations that may influence compliance with evidence-based guidelines for acute low back pain. OBJECTIVE To assess whether physicians' management decisions are consistent with the Agency for Health Research Quality's guideline and whether responses varied with the presentation of sciatica or by physician characteristics. DESIGN Cross-sectional study using a mailed survey. PARTICIPANTS Participants were randomly selected from internal medicine, family practice, general practice, emergency medicine, and occupational medicine specialties. MEASUREMENTS A questionnaire asked for recommendations for 2 case scenarios, representing patients without and with sciatica, respectively. RESULTS Seven hundred and twenty surveys were completed (response rate=25%). In cases 1 (without sciatica) and 2 (with sciatica), 26.9% and 4.3% of physicians fully complied with the guideline, respectively. For each year in practice, the odds of guideline noncompliance increased 1.03 times (95% confidence interval [CI]=1.01 to 1.05) for case 1. With occupational medicine as the referent specialty, general practice had the greatest odds of noncompliance (3.60, 95% CI=1.75 to 7.40) in case 1, followed by internal medicine and emergency medicine. Results for case 2 reflected the influence of sciatica with internal medicine having substantially higher odds (vs case 1) and the greatest odds of noncompliance of any specialty (6.93, 95% CI=1.47 to 32.78), followed by family practice and emergency medicine. CONCLUSIONS A majority of primary care physicians continue to be noncompliant with evidence-based back pain guidelines. Sciatica dramatically influenced clinical decision-making, increasing the extent of noncompliance, particularly for internal medicine and family practice. Physicians' misunderstanding of sciatica's natural history and belief that more intensive initial management is indicated may be factors underlying the observed influence of sciatica.
Appropriate Critical Values When Testing for a Single Multivariate Outlier by Using the Mahalanobis Distance

The Mahalanobis distance is a well-known criterion which may be used for detecting outliers in multivariate data. However, there are some discrepancies about which critical values are suitable for this purpose. Following a comparison with Wilks's method, this paper shows that the previously recommended {p(n-1)/(n-p)}F p,n−p are unsuitable, and p(n-1) 2 F p,n−p−1 /n(n−p−1+pF p,n−p−1 ) are the correct critical values when searching for a single outlier The importance of which critical values should be used is illustrated when searching for a single outlier in a clinical laboratory data set containing 10 patients and five variables. The jackknifed Mahalanobis distance is also discussed and the relevant critical values are given. Finally, upper bounds for the usual Mahalanobis distance and the jackknifed version are discussed.
How to calculate sample size in animal studies

Researcher must calculate the sample size before starting of any animal study. It should be adequate enough to detect a small significant difference between the groups. Small sample size is not only responsible for the insignificant result but also for the less power of the study. Calculation of sample size involves complex statistics but it can be simplified to help the researchers who are not from statistical background.
On the Theory and Computation of Evolutionary Distances

This paper gives a formal definition of the biological concept of evolutionary distance and an algorithm to compute it. For any set S of finite sequences of varying lengths this distance is a real-valued function on $S \times S$, and it is shown to be a metric under conditions which are wide enough to include the biological application. The algorithm, introduced here, lends itself to computer programming and provides a method to compute evolutionary distance which is shorter than the other methods currently in use.
Over 30% efficient InGaP/GaAs tandem solar cells

A two-terminal monolithic InGaP/GaAs tandem solar cell with a new efficiency record of 30.28% is realized with a practical large area of 4 cm2 under one-sun air-mass 1.5 global illumination. We report improvements of the tandem cell performance by introducing a double-hetero (hereafter DH) structure InGaP tunnel junction, in which the InGaP layers are surrounded by high band gap AlInP barriers. The DH structure by AlInP barriers increase the peak current of InGaP tunnel junction. The AlInP barrier directly below the InGaP top cell, which takes the part of a back surface field (hereafter BSF) layer, is found to be considerably effective in reflecting minority carriers in the top cell. The AlInP BSF layer does not only form a high potential barrier but also prevents the diffusion of zinc from a high doped tunnel junction toward the top cell during epitaxial growth. Furthermore, an InGaP tunnel junction reduces the absorption loss, which exists in a GaAs tunnel junction, and increases the photogenerated curr...
Electrical, optical, and structural properties of indium-tin-oxide thin films for organic light-emitting devices

High-quality indium–tin–oxide (ITO) thin films (200–850 nm) have been grown by pulsed laser deposition (PLD) on glass substrates without a postdeposition annealing treatment. The structural, electrical, and optical properties of these films have been investigated as a function of target composition, substrate deposition temperature, background gas pressure, and film thickness. Films were deposited from various target compositions ranging from 0 to 15 wt % of SnO2 content. The optimum target composition for high conductivity was 5 wt % SnO2+95 wt % In2O3. Films were deposited at substrate temperatures ranging from room temperature to 300 °C in O2 partial pressures ranging from 1 to 100 mTorr. Films were deposited using a KrF excimer laser (248 nm, 30 ns full width at half maximum) at a fluence of 2 J/cm2. For a 150-nm-thick ITO film grown at room temperature in an oxygen pressure of 10 mTorr, the resistivity was 4×10−4 Ω cm and the average transmission in the visible range (400–700 nm) was 85%. For a 170-n...