Miracle-dz/UniFAR-FTUs huggingface dataset:
Identification of a novel cellulose‐binding domain the multidomain 120 kDa xylanase XynA of the hyperthermophilic bacterium Thermotoga maritima

A segment of Thermotoga maritima strain MSB8 chromosomal DNA was isolated which encodes an endo‐1,4‐β‐D‐xylanase, and the nucleotide sequence of the xylanase gene, designated xynA, was determined. With a half‐life of about 40 min at 90°C at the optimal pH of 6.2, purified recombinant XynA is one of the most thermostable xylanases known. XynA is a 1059‐amino‐acid (˜120 kDa) modular enzyme composed of an N‐terminal signal peptide and five domains, in the order A1‐A2‐B‐C1‐C2. By comparison with other xylanases of family 10 of glycosyl hydrolases, the central ˜340‐amino‐acid part (domain B) of XynA represents the catalytic domain. The N terminal ˜150‐amino‐acid repeated domains (A1‐A2) have no significant similarity to the C‐terminal ˜170‐amino‐acid repeated domains (C1‐C2). Cellulose‐binding studies with truncated XynA derivatives and hybrid proteins indicated that the C‐terminal repeated domains mediate the binding of XynA to microcrystalline cellulose and that C2 alone can also promote cellulose binding. C1 and C2 did not share amino acid sequence similarity with any other known cellulose‐binding domain (CBD) and thus are CBDS of a novel type. Structurally related protein segments which are probably also CBDs were found in other multi‐domain xylanolytic enzymes. Deletion of the N‐terminal repeated domains or of all the non‐catalytic domains resulted In substantially reduced tbermostability while a truncated xylanase derivative lacking the C‐terminal tandem repeat was as thermostable as the full‐length enzyme. It is argued that the multidomain organization of some enzymes may be one of the strategies adopted by thermophiles to protect their proteins against thermal denaturation.
Attitudes Toward Quality of Survival

The purpose of this study was to examine attitudes toward the duration of survival in different health states. Health professionals were asked to consider hypothetical situ ations in which a specified period of time would be spent in a defined health state. Preferences for these different situations were assessed using two methods—a Pref erence Questionnaire and a Certainty Equivalence method. The results obtained indicated that attitudes toward duration of survival depended strongly on the amount of time to be spent in a hypothetical health state, and on the quality of the state. As the duration of survival increased, or the state under consideration became more dysfunctional, a higher proportion of raters expressed a preference for imme diate death over further survival in the dysfunctional state. These results contradict the view that time preference curves always increase monotonically, independent of the quality of survival. Instead, subjects appeared to identify a variable, the "maxi mal endurable time" in a given state. When this time was exceeded, attitudes toward additional increments of survival changed dramatically. (Med Decis Making 2:299-309, 1982)
Sleep Stage Assessment Using Power Spectral Indices of Heart Rate Variability With a Simple Algorithm

Clinical researchers do not typically assess sleep with polysomnography (PSG) but rather with observation. However, methods relying on observation have limited reliability and are not suitable for assessing sleep depth and cycles. The purpose of this methodological study was to compare a sleep analysis method based on power spectral indices of heart rate variability (HRV) data to PSG. PSG and electrocardiography data were collected synchronously from 10 healthy women (ages 20–61 years) over 23 nights in a laboratory setting. HRV was analyzed for each 60-s epoch and calculated at 3 frequency band powers (very low frequency [VLF]-hi: 0.016–0.04 Hz; low frequency [LF]: 0.04–0.15 Hz; and high frequency [HF]: 0.15–0.4 Hz). Using HF/(VLF-hi + LF + HF) value, VLF-hi, and heart rate (HR) as indices, an algorithm to categorize sleep into 3 states (shallow sleep corresponding to Stages 1 & 2, deep sleep corresponding to Stages 3 & 4, and rapid eye movement [REM] sleep) was created. Movement epochs and time of sleep onset and wake-up were determined using VLF-hi and HR. The minute-by-minute agreement rate with the sleep stages as identified by PSG and HRV data ranged from 32 to 72% with an average of 56%. Longer wake after sleep onset (WASO) resulted in lower agreement rates. The mean differences between the 2 methods were 2 min for the time of sleep onset and 6 min for the time of wake-up. These results indicate that distinguishing WASO from shallow sleep segments is difficult using this HRV method. The algorithm's usefulness is thus limited in its current form, and it requires additional modification.
On channel estimation in DTMB standard using time domain PN sequences

In some OFDM systems, time domain CP (cyclic prefix) and scattered pilots are used for synchronization and channel estimation. While in novel OFDM broadcasting systems, such as China Digital Terrestrial Multimedia Broadcasting Standard (DTMB), PN sequences rather than cyclic prefixes are inserted as guard interval between N-point IFFT blocks, which are also used as training symbols. This paper proposed a frequency domain transform method for channel estimation in time domain PN based OFDM systems. With simulation results, comparing to LS-DFT method that using scattered pilots for channel estimation, it is shown that our proposed method can provide satisfactory performance in time domain PN based terrestrial television broadcasting standard.
Osteopontin stimulates invasion of NCI‐h295 cells but is not associated with survival in adrenocortical carcinoma

Gene array studies indicated that osteopontin (OPN) mRNA is highly expressed in adrenocortical carcinomas (ACCs). OPN enhances invasiveness, proliferation, and metastasis formation, and is associated with poor survival in some malignant diseases. Integrin αvβ3 has been shown to mediate OPN effects on invasion. In this study, we demonstrated OPN and integrin αvβ3 expression in normal adrenal glands and benign adenomas, with staining seen exclusively in adrenocortical cells as well as even stronger staining in ACC. Western blot analysis confirmed overexpression of OPN in ACC (p < 0.01). With Matrigel invasion assays, we have shown that OPN greatly stimulates the invasiveness of NCI‐h295 cells (>six‐fold increase, p < 0.001). Transfection with integrin αvβ3 further increased invasiveness after OPN stimulation (p < 0.001). This increase was reversed by the addition of an anti‐integrin β3 antibody, indicating a functional relationship of OPN and integrin αvβ3 in ACC. With tissue arrays, we confirmed high OPN expression in 147 ACC samples. However, no association with survival was seen in Kaplan‐Meier analysis including 111 patients with primary tumours graded for OPN staining and follow‐up data available. In conclusion, our in vitro data indicate that OPN and integrin αvβ3 may act as a functional complex facilitating the invasiveness of adrenocortical tumours. This relationship remains of relevance to our understanding of carcinogenesis, but further studies are needed to address the physiological and pathological function of OPN in adrenal tissue. Copyright © 2009 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
Management of Childhood Hyperopia: A Pediatric Optometrist's Perspective

Purpose. To provide an optometric perspective on the management of hyperopia in children without strabismus or amblyopia. Methods. Factors that have potentially shaped optometry's viewpoint and influenced its prescribing philosophy for childhood hyperopia, such as optometry school and residency training, professional association clinical guidelines, conferences and continuing education courses, textbooks, scientific studies, opinions of professional leaders, and clinical experiences are discussed. Results. Variations in prescribing patterns for childhood hyperopia occur within optometry and within ophthalmology. There are also differences in prescribing philosophies between the two professions. These differences are probably due to a greater level of concern, more so among optometrists, about associated vision functions such as accommodation, vergence, and stereopsis, as well as concerns about the potential impact of uncorrected hyperopia on reading and school performance. Conclusions. If indications for prescribing spectacles for children with hyperopia are to be validated, randomized controlled trials need to be performed.
Optimization of targeted RNA recombination and mapping of a novel nucleocapsid gene mutation in the coronavirus mouse hepatitis virus

We have recently described a method of introducing site-specific mutations into the genome of the coronavirus mouse hepatitis virus (MHV) by RNA recombination between cotransfected genomic RNA and a synthetic subgenomic mRNA (C. A. Koetzner, M. M. Parker, C. S. Ricard, L. S. Sturman, and P. S. Masters, J. Virol. 66:1841-1848, 1992). By using a thermolabile N protein mutant of MHV (Alb4) as the recipient virus and synthetic RNA7 (the mRNA for the nucleocapsid protein N) as the donor, we selected engineered recombinant viruses as heat-stable progeny resulting from cotransfection. We have now been able to greatly increase the efficiency of targeted recombination in this process by using a synthetic defective interfering (DI) RNA in place of RNA7. The frequency of recombination is sufficiently high that, with Alb4 as the recipient, recombinants can be directly identified without using thermal selection. The synthetic DI RNA has been used to demonstrate that the lesion in another temperature-sensitive and thermolabile MHV mutant, Alb1, maps to the N gene. Sequencing of the Alb1 N gene revealed two closely linked point mutations that fall in a region of the N molecule previously noted as being the most highly conserved region among all of the coronavirus N proteins. Analysis of revertants of the Alb1 mutant revealed that one of the two mutations is critical for the temperature-sensitive phenotype; the second mutation is phenotypically silent.
Soccer Fatigue, Sprinting and Hamstring Injury Risk

The aim of this study was to investigate the effect of a multi-directional soccer-specific fatigue protocol on sprinting kinematics in relation to hamstring injury risk. Nine semi-professional soccer players (Mean +/- SD: Age: 21.3 +/- 2.9 year; Height 185.0 +/- 8.7 cm; Body Mass 81.6 +/- 6.7 kg) completed the SAFT(90); a multi-directional, intermittent 90 min exercise protocol representative of soccer match-play. The 10m sprint times and three-dimensional kinematic data were recorded using a high-speed motion capture system (Qualisys Track Manager) every 15 min during the SAFT(90). A significant time dependent increase was observed in sprint time during the SAFT(90) (P<0.01) with a corresponding significant decrease in stride length (P<0.01). Analysis of the kinematic sprint data revealed significantly reduced combined maximal hip flexion and knee extension angle, indicating reduced hamstring length, between pre-exercise and half-time (P<0.01) and pre-exercise and full-time (P<0.05). These findings revealed that the SAFT(90) produced time dependent impairments in sprinting performance and kinematics of technique which may result from shorter hamstring muscle length. Alterations in sprinting technique may have implications for the increased predisposition to hamstring strain injury during the latter stages of soccer match-play.
Effective Control of Salmonella Infections by Employing Combinations of Recombinant Antimicrobial Human β-Defensins hBD-1 and hBD-2

ABSTRACT We successfully produced two human β-defensins (hBD-1 and hBD-2) in bacteria as functional peptides and tested their antibacterial activities against Salmonella enterica serovar Typhi, Escherichia coli, and Staphylococcus aureus employing both spectroscopic and viable CFU count methods. Purified peptides showed approximately 50% inhibition of the bacterial population when used individually and up to 90% when used in combination. The 50% lethal doses (LD50) of hBD-1 against S. Typhi, E. coli, and S. aureus were 0.36, 0.40, and 0.69 μg/μl, respectively, while those for hBD-2 against the same bacteria were 0.38, 0.36, and 0.66 μg/μl, respectively. Moreover, we observed that bacterium-derived antimicrobial peptides were also effective in increasing survival time and decreasing bacterial loads in the peritoneal fluid, liver, and spleen of a mouse intraperitoneally infected with S. Typhi. The 1:1 hBD-1/hBD-2 combination showed maximum effectiveness in challenging the Salmonella infection in vitro and in vivo. We also observed less tissue damage and sepsis formation in the livers of infected mice after treatment with hBD-1 and hBD-2 peptides individually or in combination. Based on these findings, we conclude that bacterium-derived recombinant β-defensins (hBD-1 and hBD-2) are promising antimicrobial peptide (AMP)-based substances for the development of new therapeutics against typhoid fever.
Human Ca2+/Calmodulin-dependent Protein Kinase Kinase β Gene Encodes Multiple Isoforms That Display Distinct Kinase Activity*

Ca+2/calmodulin-dependent protein kinases (CaMKs) are activated upon binding of Ca+2/calmodulin. To gain maximal activity, CaMK I and CaMK IV can be further phosphorylated by an upstream kinase, CaMK kinase (CaMKK). We previously isolated cDNA clones encoding human CaMKK β isoforms that are heterogeneous in their 3′-sequences (Hsu, L.-S., Tsou, A.-P., Chi, C.-W., Lee, C.-H., and Chen, J.-Y. (1998)J. Biomed. Sci. 5, 141–149). In the present study, we examined the genomic organization and transcription of the humanCaMKK β gene. The human CaMKK β locus spans more than 40 kilobase pairs and maps to chromosome 12q24.2. It is organized into 18 exons and 17 introns that are flanked by typical splice donor and acceptor sequences. Two major species of transcripts, namely the β1 (5.6 kilobase pairs) and β2 (2.9 kilobase pairs), are generated through differential usage of polyadenylation sites located in the last and penultimate exons. Additional forms ofCaMKK β transcripts were also identified that resulted from alternative splicing of the internal exons 14 and/or 16. These isoforms display differential expression patterns in human tissues and tumor-derived cell lines. They also exhibit a distinct ability to undergo autophosphorylation and to phosphorylate the downstream kinases CaMK I and CaMK IV. The differential expression of CaMKK β isoforms with distinct activity further suggests the complexity of the regulation of the CaMKK/CaMK cascade and an important role for CaMKK in the action of Ca+2-mediated cellular responses.
Achilles tendon (TA) size and power Doppler ultrasound (PD) changes compared to MRI: a preliminary observational study.

AIM To assess whether abnormal Achilles tendon (TA) magnetic resonance imaging (MRI) and spectral ultrasound (US) features have associated development of microvascular power Doppler (PD) flow. MATERIALS AND METHODS In a prospective, controlled and blinded study six patients with TA symptoms were compared to five with other ankle abnormalities. Two radiologists independently measured the mean maximal anteroposterior diameter on MRI and conventional US (categorized as normal <6 mm, mild 6.1-10 mm, moderate 1.1-1.5 cm and severely enlarged > 1.6 cm), assessed morphology and studied the vessels using power Doppler. They formed a consensus over discrepancies. Sonography of the contralateral side within 24 h was used as a control. RESULTS Twenty-one tendons in six women and five men, aged 45-77 years (mean 57.6 years), were examined, 12 tendons were of normal US morphology and size (< 6 mm), and did not exhibit PD's flow (interobserver agreement K > 0.74). Of the 12 tendons studied by MRI five were normal, seven tendons were enlarged, five of which had a proportionate increase in PD flow at the margin on the deep surface and four also had vessels in the centre of the tendon. All five of these tendons had high signal on T2-weighting (T2W). Of the two mildly enlarged tendons of intermediate signal on T1 and T2W, one showed PD flow and the other did not. CONCLUSIONS In patients with TA disease power Doppler ultrasound shows proliferation of vessels in enlarged, abnormal tendons demonstrated on MRI and standard ultrasound, in the absence of definite tears.
Improved target detection through extended dwell time algorithm

Output signal-to-interference-plus-noise ratio (SINR) can be increased by extending the dwell time or coherent processing interval (CPI) over which target signal energy is integrated. However, over a long dwell time, nonlinear phase components in the slow-time signal limit the effectiveness of traditional Fourier-based processing methods to coherently integrate signal energy; thus, signal energy is often coherently integrated on a sub-CPI basis. This paper investigates a new extended dwell temporal signal processing algorithm that utilizes the signal energy in adjacent sub-CPIs in a unique way to improve the detection of weak, slow-moving targets. In many cases, the extended dwell algorithm more than doubles the probability of detection of low radial velocity targets over conventional noncoherent integration.
Association of CLOCK, ARNTL, and NPAS2 gene polymorphisms and seasonal variations in mood and behavior

Seasonal affective disorder (SAD) is a condition of seasonal mood changes characterized by recurrent depression in autumn or winter that spontaneously remits in spring or summer. Evidence has suggested that circadian gene variants contribute to the pathogenesis of SAD. In this study, we investigated polymorphisms in the CLOCK, ARNTL, and NPAS2 genes in relation to seasonal variation in 507 healthy young adults. Seasonal variations were assessed with the Seasonality Pattern Assessment Questionnaire. The prevalence of SAD was 12.0% (winter-type 9.3%, summer-type 2.8%). No significant difference was found between the groups in the genotype distribution of ARNTL rs2278749 and NPAS2 rs2305160. The T allele of CLOCK rs1801260 was significantly more frequent in seasonals (SAD + subsyndromal SAD) compared with non-seasonals (p = 0.020, odds ratio = 1.89, 95% confidence interval = 1.09–3.27). Global seasonality score was significantly different among genotypes of CLOCK rs1801260, but not among genotypes of ARNTL rs2278749 and NPAS2 rs2305160. However, statistical difference was observed in the body weight and appetite subscales among genotypes of ARNTL rs2278749 and in the body weight subscale among genotypes of NPAS2 rs2305160. There was synergistic interaction between CLOCK rs1801260 and ARNTL rs2278749 on seasonality. To our knowledge, this study is the first to reveal an association between the CLOCK gene and seasonal variations in mood and behavior in the Korean population. Although we cannot confirm previous findings of an association between SAD and the ARNTL and NPAS2 genes, these genes may influence seasonal variations through metabolic factors such as body weight and appetite. The interaction of the CLOCK and ARNTL genes contributes to susceptibility for SAD.
Basic experimental study on helical antennas of wireless power transfer for Electric Vehicles by using magnetic resonant couplings

Wireless power transfer is required for the diffusion of Electric Vehicles (EVs) because it makes possible the process of automatically charging EVs. The technology of wireless power transfer requires three main elements: large air gaps, high efficiency and a large amount of power. Though, there has been no such technology, recently, the technology of electromagnetic resonant couplings was proposed and named WiTricity. With this technology there are large air gaps, high efficiency and large amounts of power. In this paper, the feasibility of wireless power transfer for EVs by electromagnetic resonance coupling is studied. We studied small sized antennas that can be equipped on the bottom of a vehicle and we studied the electrical characteristics of the antenna with equivalent circuits, electromagnetic analysis and experimentation. The length of the air gaps between a transmitting antenna and a receiving antenna affect resonance frequencies. The resonance frequency changes from two to one depending on the length of the air gap. Until a certain distance, maximum efficiencies are not changed. Large air gaps are weak couplings. In a weak coupling at resonance, magnetic resonance couplings can transfer energy with high efficiency. The specification results at high power are proposed. In this paper, the feasibility of wireless power transfer with large air gaps and high efficiency by small sized antennas that can be equipped on the bottom of EVs is proposed.
Saliency Benchmarking: Separating Models, Maps and Metrics

The field of fixation prediction is heavily model-driven, with dozens of new models published every year. However, progress in the field can be difficult to judge because models are compared using a variety of inconsistent metrics. As soon as a saliency map is optimized for a certain metric, it is penalized by other metrics. Here we propose a principled approach to solve the benchmarking problem: we separate the notions of saliency models and saliency maps. We define a saliency model to be a probabilistic model of fixation density prediction and, inspired by Bayesian decision theory, a saliency map to be a metric-specific prediction derived from the model density which maximizes the expected performance on that metric. We derive the optimal saliency map for the most commonly used saliency metrics (AUC, sAUC, NSS, CC, SIM, KL-Div) and show that they can be computed analytically or approximated with high precision using the model density. We show that this leads to consistent rankings in all metrics and avoids the penalties of using one saliency map for all metrics. Under this framework, "good" models will perform well in all metrics.
Clinical features and outcome of initially unresected nonmetastatic pediatric nonrhabdomyosarcoma soft tissue sarcoma.

PURPOSE To describe the clinical features, response to therapy, and outcome of pediatric patients with initially unresected nonmetastatic nonrhabdomyosarcoma soft tissue sarcoma (NRSTS). PATIENTS AND METHODS We retrospectively reviewed the presenting clinical features and tumor characteristics of all 40 pediatric patients with initially unresected nonmetastatic NRSTS who were seen at our institution between March 1962 and December 1996. A subset of 27 patients for whom complete treatment information was available was analyzed to determine whether response to therapy was associated with local disease control and event-free and overall survival. RESULTS More than 70% of the 40 patients had tumors with high-risk features (tumor size > 5 cm, high grade, invasiveness). For the 27 patients included in the outcome analysis, 5-year event-free survival and survival estimates were 33% +/- 9% and 56% +/- 10%, respectively. Ten (37%) of these patients had a complete or partial response to neoadjuvant chemotherapy and/or radiotherapy, and only two of the 10 had residual tumor after surgery. Combined chemotherapy and radiotherapy seemed more effective than either modality alone in inducing a response, but the response to neoadjuvant therapy did not predict outcome. Most treatment failures were local, and postrelapse survival was poor (19% +/- 10%). CONCLUSION Initially unresected NRSTS constitutes a unique subgroup of pediatric sarcomas that commonly present with high-risk features and respond poorly to neoadjuvant therapy. Only about one third of patients treated with multimodal therapy remain disease-free, and local control is the major limiting factor in achieving cure. More effective risk-directed treatments are needed for this unique subgroup of patients.