Miracle-dz/UniFAR-FTUs huggingface dataset:
Mitochondrial and DNA damage in bovine somatic cell nuclear transfer embryos

The generation of reactive oxygen species (ROS) and subsequent mitochondrial and DNA damage in bovine somatic cell nuclear transfer (SCNT) embryos were examined. Bovine enucleated oocytes were electrofused with donor cells and then activated by a combination of Ca-ionophore and 6-dimethylaminopurine culture. The H2O2 and ˙OH radical levels, mitochondrial morphology and membrane potential (ΔΨ), and DNA fragmentation of SCNT and in vitro fertilized (IVF) embryos at the zygote stage were analyzed. The H2O2 (35.6 ± 1.1 pixels/embryo) and ˙OH radical levels (44.6 ± 1.2 pixels/embryo) of SCNT embryos were significantly higher than those of IVF embryos (19.2 ± 1.5 and 23.8 ± 1.8 pixels/embryo, respectively, p < 0.05). The mitochondria morphology of SCNT embryos was diffused within the cytoplasm. The ΔΨ of SCNT embryos was significantly lower (p < 0.05) than that of IVF embryos (0.95 ± 0.04 vs. 1.21 ± 0.06, red/green). Moreover, the comet tail length of SCNT embryos was longer than that of IVF embryos (515.5 ± 26.4 µm vs. 425.6 ± 25.0 µm, p < 0.05). These results indicate that mitochondrial and DNA damage increased in bovine SCNT embryos, which may have been induced by increased ROS levels.
End-user acceptance of a cloud-based teledentistry system and Android phone app for remote screening for oral diseases

Objective This study aimed to evaluate users’ acceptance of a teledentistry model utilizing a smartphone camera used for dental caries screening and to identify a number of areas for improvement of the system. Methods A store-and-forward telemedicine platform “Remote-I” was developed to assist in the screening of oral diseases using an image acquisition Android app operated by 17 teledental assistants. A total of 485 images (five images per case) were directly transmitted from the Android app to the server. A panel of five dental practitioners (graders) assessed the images and reported their diagnosis. A user acceptance survey was sent to the graders and smartphone users following completion of the screening program. Results Of the 22 surveys sent out, 20 (91%) were completed. Generally, users showed optimism towards the use of the teledentistry system, and strongly positively assessed items on content and service quality. The majority of graders took less than 15 min to read the images while phone users took 5–10 min to complete the dental photography using the Android app. This study identified a number of factors that are essential for improving the current system, such as optimization of smartphone camera features, the format of the server, and the orientation of images and using oral retractors during photography. Conclusions Users appear to be generally satisfied with the proposed teledentistry model. However, they have specific concerns to address, many of which could be resolved through more effective training, coordination between sites and upgrading the current system.
Snail susceptibility to crab predation : A case study of co-evolution from Lake Tanganyika , East Africa

Co-evolution has been invoked as an explanation for Lake Tanganyika’s unusual endemic fauna. The crabs Platytelphusa armata and Potamonautes platynotus are molluscivores, found in the same habitats as the gastropods Lavigeria coronata, L. grandis, and L. nassa (West & Cohen 1994). As these are the largest gastropods in the Lavigeria species flock, and often the most exposed, we are determining whether shell size and sculpture provides protection from predation. We are also attempting to reveal the effectiveness of chela morphology among crab predators. The fine details of the predator-prey relationships will link the ecological processes with their potential evolutionary patterns.
The role of epigenetics in cognitive ageing

As the population is ageing, a better understanding of the underlying causes of age‐related cognitive decline (cognitive ageing) is required. Epigenetic dysregulation is proposed as one of the underlying mechanisms for cognitive ageing. We review the current knowledge on epigenetics and cognitive ageing and appraise the potential of epigenetic preventative and therapeutic interventions.
Through Silicon Via (TSV) Defect Modeling, Measurement, and Analysis

Through silicon via (TSV)-based 3-D integrated circuit has introduced the solution to limitlessly growing demand on high system bandwidth, low power consumption, and small form factor of electronic devices. As the system design aims for higher performance, the physical dimensions of the channels are continuously decreasing. With TSV diameter of less than 10 μm and pitch of several tens of micrometers, the I/O count has increased up to the order of tens of thousands for wide bandwidth data transmission. However, without highly precise fabrication process, such small structures are susceptible to a variety of defects. For the first time, in this paper, we propose a noninvasive defect analysis method for high-speed TSV channel. With designed and fabricated test vehicles, the proposed method is demonstrated with S-parameter and time-domain reflectometry measurement results. In addition, we present equivalent circuit models of TSV daisy-chain structures, including the circuit components for open defect and short defect. With characterized dominant factors in each frequency range, S11 is analyzed to distinguish and locate the defects by the amount of capacitance, resistance, and inductance that the signal experiences. S-parameter measurement sufficiently allows high-frequency defect analysis of TSV channel without destroying the test sample. We experimentally verified the accuracy of the suggested model by comparing the S-parameter results from circuit simulations and measurements. Finally, the model is modified to discuss the effects of open defect and short defect on the electrical characteristics of TSV channel.
Multi retention level STT-RAM cache designs with a dynamic refresh scheme

Spin-transfer torque random access memory (STT-RAM) has received increasing attention because of its attractive features: good scalability, zero standby power, non-volatility and radiation hardness. The use of STT-RAM technology in the last level on-chip caches has been proposed as it minimizes cache leakage power with technology scaling down. Furthermore, the cell area of STT-RAM is only 1/9 ∼ 1/3 that of SRAM. This allows for a much larger cache with the same die footprint, improving overall system performance through reducing cache misses. However, deploying STT-RAM technology in L1 caches is challenging because of the long and power-consuming write operations. In this paper, we propose both L1 and lower level cache designs that use STT-RAM. In particular, our designs use STTRAM cells with various data retention time and write performances, made possible by different magnetic tunneling junction (MTJ) designs. For the fast STT-RAM bits with reduced data retention time, a counter controlled dynamic refresh scheme is proposed to maintain the data validity. Our dynamic scheme saves more than 80% refresh energy compared to the simple refresh scheme proposed in previous works. A L1 cache built with ultra low retention STTRAM coupled with our proposed dynamic refresh scheme can achieve 9.2% in performance improvement, and saves up to 30% of the total energy when compared to one that uses traditional SRAM. For lower level caches with relative large cache capacity, we propose a data migration scheme that moves data between portions of the cache with different retention characteristics so as to maximize the performance and power benefits. Our experiments show that on the average, our proposed multi retention level STT-RAM cache reduces 30 ∼ 70% of the total energy compared to previous works, while improving IPC performance for both 2-level and 3-level cache hierarchy.
Adoption of biosecurity practices in the Australian poultry industries.

OBJECTIVE To determine the level of adoption within the Australian poultry industries of a range of standard biosecurity practices. DESIGN A questionnaire survey of owners and managers of 1753 commercial poultry farms. Procedure Information was collected by telephone or in person from the owners and managers of poultry farms. Data were entered onto an Excel spreadsheet and analysed using the statistical tools within Excel. RESULTS The response rates to the questionnaire for the chicken meat, egg, duck and turkey sectors were 94%, 37%, 92% and 96% respectively. Within the chicken meat sector, the adoption rate exceeded 98% for 11 practices with only the rates for appropriate disposal of spent litter/manure (94%) and development of farm level biosecurity plans (88%) falling below this level. Adoption rates for all practices had increased or remained at 100% since the last survey conducted in 2001. Integrated companies in the turkey and duck sector also reported high levels of adoption for most biosecurity practices although rates for the use of fresh litter, cleaning of sheds between batches of birds and maintenance of single age flocks were lower than in the chicken meat sector. Adoption rates for biosecurity practices on independently owned farms in the turkey and duck sectors were lower than for farms operated by integrated companies. CONCLUSIONS Farms in the chicken meat, turkey and duck sectors of the Australian poultry industries have a high level of adoption of biosecurity practices with only a small proportion of farms needing to further enhance their biosecurity.
Pathological grading of regression following neoadjuvant chemoradiation therapy: the clinical need is now

Neoadjuvant chemoradiotherapy for locally advanced rectal cancer has been shown to decrease rates of local recurrence and more than double the rate of sphincter-preserving surgery. There is now compelling evidence that pathological complete response is an independent predictor of likelihood of local recurrence, distal metastases, disease-free and overall survival in locally advanced rectal cancer following neoadjuvant chemoradiotherapy. Pathological regression grading can therefore guide clinical decisions about salvage surgical strategies, adjuvant therapy and long-term surveillance. No universally recognised regression grading system currently exists for pathologists presented with resected tumour specimens following neoadjuvant chemoradiotherapy. The purpose of this review is to highlight the relevance of accurate tumour regression grading in achieving optimal clinical care for patients with rectal cancer.
Activation of mouse lymphocytes by anti-immunoglobulin. II. A thymus- independent response by a mature subset of B lymphocytes

Mouse spleen cells can be stimulated to proliferate in vitro by purified anti-mu or anti-gamma,kappa antibodies. These responses can be obtained in cell populations bearing membrane immunoglobulin (Ig), purified by the fluorescence activated cell sorter (FACS), but they are not observed in FACS-purified Ig- cell populations. Furthermore, treatment of spleen cell populations with anti-Thy 1.2 and complement does not impair the response, nor does addition of nylon wool-purified T lymphocytes enhance it. These results indicate that B lymphocytes respond to anti-Ig and that their response does not require T cells. On the other hand, cells from athymic nude (nu/nu) mice respond slightly less well to anti-mu than do cells from heterozygous littermate (nu/+) controls; nu/nu cells are almost unresponsive to anti-gamm,kappa and addition of nylon wool-purified T cells from nu/+ controls does not restore the response. This suggests that T lymphocytes or the thymus may control the appearance of cells responsive to anti-gamma,kappa. Responsiveness of normal mice to anti-mu does not appear until 4 wk of age and does not reach maximum levels until 8 wk of age. Acquisition of full responsiveness to anti-gamma,kappa is even more delayed. This, together with the failure of mice with the CBA/N B-cell defect to respond to anti-Ig, suggests that cells stimulated to proliferate by anti-Ig are a mature subset of B cells. Depletion of adherent cells by Sephadex G-10 treatment or by treatment with carbonyl iron and exposure to a magnetic field does not diminish anti-mu or anti-gamma,kappa responses, suggesting that the responsiveness does not require the presence of macrophages. Thus, activation of B-cell proliferation by anti-Ig appears to be a T-cell independent, macrophage-independent process in which membrane Ig plays a direct role in signal generation.
Acid- and Base-Induced Proteins during Aerobic and Anaerobic Growth of Escherichia coli Revealed by Two-Dimensional Gel Electrophoresis

ABSTRACT Proteins induced by acid or base, during long-term aerobic or anaerobic growth in complex medium, were identified inEscherichia coli. Two-dimensional gel electrophoresis revealed pH-dependent induction of 18 proteins, nine of which were identified by N-terminal sequencing. At pH 9, tryptophan deaminase (TnaA) was induced to a high level, becoming one of the most abundant proteins observed. TnaA may reverse alkalinization by metabolizing amino acids to produce acidic products. Also induced at high pH, but only in anaerobiosis, was glutamate decarboxylase (GadA). Thegad system (GadA/GadBC) neutralizes acidity and enhances survival in extreme acid; its induction during anaerobic growth may help protect alkaline-grown cells from the acidification resulting from anaerobic fermentation. To investigate possible responses to internal acidification, cultures were grown in propionate, a membrane-permeant weak acid which acidifies the cytoplasm. YfiD, a homologue of pyruvate formate lyase, was induced to high levels at pH 4.4 and induced twofold more by propionate at pH 6; both of these conditions cause internal acidification. At neutral or alkaline pH, YfiD was virtually absent. YfiD is therefore a strong candidate for response to internal acidification. Acid or propionate also increased the expression of alkyl hydroperoxide reductase (AhpC) but only during aerobic growth. At neutral or high pH, AhpC showed no significant difference between aerobic and anaerobic growth. The increase of AhpC in acid may help protect the cell from the greater concentrations of oxidizing intermediates at low pH. Isocitrate lyase (AceA) was induced by oxygen across the pH range but showed substantially greater induction in acid or in base than at pH 7. Additional responses observed included the induction of MalE at high pH and induction of several enzymes of sugar metabolism at low pH: the phosphotransferase system components ManX and PtsH and the galactitol fermentation enzyme GatY. Overall, our results indicate complex relationships between pH and oxygen and a novel permeant acid-inducible gene, YfiD.
Stereoselectivity of Pseudomonas cepacia lipase toward secondary alcohols: A quantitative model

The lipase from Pseudomonas cepacia represents a widely applied catalyst for highly enantioselective resolution of chiral secondary alcohols. While its stereopreference is determined predominantly by the substrate structure, stereoselectivity depends on atomic details of interactions between substrate and lipase. Thirty secondary alcohols with published E values using P. cepacia lipase in hydrolysis or esterification reactions were selected, and models of their octanoic acid esters were docked to the open conformation of P. cepacia lipase. The two enantiomers of 27 substrates bound preferentially in either of two binding modes: the fast‐reacting enantiomer in a productive mode and the slow‐reacting enantiomer in a nonproductive mode. Nonproductive mode of fast‐reacting enantiomers was prohibited by repulsive interactions. For the slow‐reacting enantiomers in the productive binding mode, the substrate pushes the active site histidine away from its proper orientation, and the distance d(HNϵ – Oalc) between the histidine side chain and the alcohol oxygen increases. d(HNϵ – Oalc) was correlated to experimentally observed enantioselectivity: in substrates for which P. cepacia lipase has high enantioselectivity (E > 100), d(HNϵ – Oalc) is>2.2 Å for slow‐reacting enantiomers, thus preventing efficient catalysis of this enantiomer. In substrates of low enantioselectivity (E < 20), the distance d(HNϵ – Oalc) is less than 2.0 Å, and slow‐ and fast‐reacting enantiomers are catalyzed at similar rates. For substrates of medium enantioselectivity (20 < E< 100), d(HNϵ – Oalc) is around 2.1 Å. This simple model can be applied to predict enantioselectivity of P. cepacia lipase toward a broad range of secondary alcohols.
Stability and localization of rapid shear in fluid‐saturated fault gouge: 1. Linearized stability analysis

Field observations of major earthquake fault zones show that shear deformation is often confined to principal slipping zones that may be of order 1–100 μm wide, located within a broader gouge layer of order 10–100 mm wide. This paper examines the possibility that the extreme strain localization observed may be due to the coupling of shear heating, thermal pressurization, and diffusion. In the absence of a stabilizing mechanism shear deformation in a continuum analysis will collapse to an infinitesimally thin zone. Two possible stabilizing mechanisms, studied in this paper, are rate‐strengthening friction and dilatancy. For rate‐strengthening friction alone, a linear stability analysis shows that uniform shear of a gouge layer is unstable for perturbations exceeding a critical wavelength. Using this critical wavelength we predict a width for the localized zone as a function of the gouge properties. Taking representative parameters for fault gouge at typical centroidal depths of crustal seismogenic zones, we predict localized zones of order 5–40 μm wide, roughly consistent with field and experimental observations. For dilatancy alone, linearized strain rate perturbations with a sufficiently large wavelength will undergo transient exponential growth before decaying back to uniform shear. The total perturbation strain accumulated during this transient strain rate localization is shown to be largely controlled by a single dimensionless parameter E, which is a measure of the dilatancy of the gouge material due to an increase in strain rate.
Topical colloidal indocyanine green-mediated photodynamic therapy for treatment of basal cell carcinoma

Abstract Indocyanine green (ICG) is a near-IR fluorescent dye with a great potential for application as photosensitizer in topical photodynamic therapy (PDT) of skin diseases. Despite its merits, its use has been hampered by its high degradation rate. Therefore, in the current article, ICG was encapsulated in a vesicular colloidal nanocarrier (transfersomes), with the aim of enhancing its therapeutic efficacy. Transfersomes were characterized for their entrapment efficiency, particle size, zeta potential, morphology, in vitro release and histopathological effect on mice skin. A pilot clinical study was conducted to test its therapeutic potential for PDT of basal cell carcinoma (BCC). Transfersomal ICG displayed particle size (∼125 nm) and a negative zeta potential (∼−31 mV). Transfersomes were also able to sustain the release of ICG >2 h. Upon incorporation of transfersomal ICG in gel form, it was found to maintain the normal histology of mice skin post-irradiation with diode laser 820 nm. Moreover, ICG transfersomal PDT achieved 80% clearance rate for BCC patients with minimal pain reported during treatment. The previous findings suggest that transfersomal nanoencapsulated ICG is a promising treatment modality for BCC.
The Changing Epidemiology of Childhood Pneumococcal Disease in Korea

The wide use of antimicrobial agents and 7-valent pneumococcal conjugate vaccine (PCV7) has led to major changes in the epidemiology of childhood pneumococcal diseases. In Korea, data on the population-based incidence of childhood invasive pneumococcal diseases (IPD) are not available; however, institution-based surveillance data suggest a substantial burden of childhood IPD. Following the introduction of the PCV7 in Korea in 2003, the proportion of IPD caused by vaccine-type pneumococci has decreased, while non-PCV7 serotypes, especially serotypes 19A and 6A, whose proportions had been increasing before the introduction of the vaccine, became predominant among childhood IPD isolates. This article reviews the overall impact of PCV7 utilization and summarizes the results obtained so far. Continuous monitoring and gathering of scientific evidence for the epidemiological transition of pneumococcal carriage and IPD will be important for the management of pneumococcal infections in Korea.
Prognostic Utility of Routine Chimerism Testing at 2 – 6 Months after Allogeneic Hematopoietic Cell Transplantation

word count: 227 Abstract The utility of routine chimerism analysis as a prognostic indicator of subsequent outcomes after allogeneic hematopoietic cell transplantation (HCT) with myeloablative conditioning regimens remains controversial. To address this controversy, routine chimerism test results at 2 – 6 months after HCT with myeloablative conditioning regimens were evaluated for association with subsequent risks of chronic graft versus host disease (GVHD), non-relapse mortality (NRM), relapse and overall mortality. Only 70 (5%) of 1304 patients had <95% donor-derived cells in the marrow. Low donor chimerism in the marrow occurred predominantly among patients with low risk disease as compared to higher risk diseases and was significantly associated with a reduced risk of chronic GVHD. Among 673 patients tested, 164 (24%) had <85% donor-derived T cells in the blood. Low donor T cell chimerism occurred predominantly among patients with low risk disease as compared to higher risk diseases, among those who had conditioning with busulfan as compared to TBI, and among those with lower grades of acute GVHD. Low donor T cell chimerism in the blood was significantly associated with a reduced risk of chronic GVHD, but not with the risks of relapse, NRM or overall mortality. Routine testing of chimerism in the marrow and blood at 2 – 6 months after HCT with myeloablative conditioning regimens may be helpful in documenting engraftment in clinical trials but provides only limited prognostic information in clinical practice.
Turning CALM into excitement: AP180 and CALM in endocytosis and disease

Dynamic flux of membrane between intracellular compartments is a key feature of all eukaryotic cells. Soluble N‐ethylmaleimide‐sensitive factor attachment protein receptors (SNAREs) play a crucial role in membrane dynamics by facilitating membrane fusion, for example at synapses where small synaptic vesicles (SVs) undergo activity‐regulated neuroexocytosis, followed by the endocytic re‐cycling of SV proteins and lipids. Recent work shows that the assembly protein 180 (AP180) N‐terminal homology (ANTH) domain containing proteins AP180 and clathrin assembly lymphoid myeloid leukaemia (CALM) not only regulate the assembly of the endocytic machinery but also act as sorters for a subset of SNAREs, the vesicle‐associated membrane proteins (VAMPs), most notably VAMP/synaptobrevin 2 at synapses. In this review, we summarise the current state of knowledge about the roles of AP180 and CALM family members in clathrin‐dependent membrane traffic, the molecular mechanistic basis for their activities and their potential involvement in human disease.