Miracle-dz/UniFAR-FTUs huggingface dataset:
The Short-FormMcGill Pain Questionnaire-Revised to Evaluate Persistent Pain and Surgery-Related Symptoms in Healthy Women Undergoing a Planned Cesarean Delivery

Background and Objectives The incidence of chronic pain after cesarean delivery (CD) has been estimated to range between 0.3% and 18%. This wide range may be explained by differing study methodologies. Furthermore, a comprehensive characterization of pain quality is lacking. The aim of this study was to evaluate persistent pain in a healthy obstetric population undergoing planned CD and to provide a comprehensive description of pain quality. Methods Three hundred eighty-one women with no pain history undergoing CD were included in this prospective, observational cohort study. Spinal anesthesia was standardized, and postoperative pain was recorded at 24 hours. In each woman, pain was assessed at 8 weeks, and 6 and 12 months using questionnaires of pain intensity and interference. Pain quality was assessed using the Short-Form McGill Pain Questionnaire–Revised. Results The incidence of persistent pain at 8 weeks was 11% (95% confidence interval, 8%–14%), with pain reported as being mild and interfering with common daily activities by 32% of women. At 6 and 12 months, the incidence was 3% (95% confidence interval, 2%–6%) and 0.6% (95% confidence interval, 0%–2%) respectively, with pain rarely interfering with daily activities. However, 22% of women described other surgery-related symptoms at 12 months. Conclusions The incidence of chronic pain at 12 months after planned CD is low (0.6%) and if present symptoms are mostly mild and not interfering with common daily activities. Using Short-Form McGill Pain Questionnaire–Revised, this study provides a comprehensive evaluation of pain quality that can be used as a basis in future post-CD pain trials.
Age-related annual decline of lung function in patients with COPD

Background According to the Fletcher–Peto curve, rate of decline in forced expiratory volume in 1-second (FEV1) accelerates as age increases. However, recent studies have not demonstrated that the rate of FEV1 decline accelerates with age among COPD patients. The objective of the study is to evaluate annual rate of FEV1 decline as age increases among COPD patients. Methods In this retrospective cohort study, we enrolled COPD patients who were followed up at two tertiary care university hospitals from January 2000 to August 2013. COPD was defined as post-bronchodilator (BD) FEV1/forced vital capacity (FVC) of <0.7. All participants had more than two spirometries, including BD response. Age groups were categorized as follows: below versus above median age or four quartiles. Results A total of 518 participants (94.2% male; median age, 67 years; range, 42–90 years) were included. Mean absolute and predictive values of post-BD FEV1 were 1.57±0.62 L and 52.53%±18.29%, respectively. Distribution of Global initiative for Chronic Obstructive Lung Disease groups did not show statistical differences between age groups categorized by two different criteria. After grouping the population by age quartiles, the rate of FEV1 decline was faster among older patients than younger ones whether expressed as absolute value (−10.60±5.57 mL/year, −15.84±6.01 mL/year, −18.63±5.53 mL/year, 32.94±6.01 mL/year, respectively; P=0.048) or predicted value (−0.34%±0.19%/year, −0.53%±0.21%/year, −0.62%±0.19%/year, −1.26%±0.21%/year, respectively, P=0.010). Conclusion As suggested conceptually by the Fletcher−Peto curve, annual FEV1 decline among COPD patients is accelerated among older patients than younger ones.
ACTIVITY-GUIDED ANTITHROMBIN III THERAPY IN SEVERE SURGICAL SEPSIS: EFFICACY AND SAFETY ACCORDING TO A RETROSPECTIVE DATA ANALYSIS

Recent controlled studies that evaluated the efficacy of an adjuvant antithrombin (AT) III therapy in severe sepsis used a uniform AT-III dose and duration of therapy and did not adjust to the actual AT-III deficit. It was the aim of the present study to explore if surgical patients with severe sepsis might have a treatment benefit from an activity-guided AT-III therapy. We performed a retrospective cohort analysis using an intensive care unit (ICU) database. To examine the effect of AT-III on outcome and on red cell transfusion rate, multivariate generalized additive models (GAMs), Cox-type additive hazard regression models, and propensity score adjustments were used. Five hundred forty-five postoperative surgical patients requiring ICU therapy because of severe sepsis were analyzed. Antithrombin III was given to those patients believed to be at a high risk of dying. Antithrombin III therapy was guided by the individual AT-III activity and aimed at the maintenance of an activity of at least 100%. Antithrombin III supplementation was discontinued after the plasma AT-III activity had been persistently normal without simultaneous AT-III infusion. We found that patients receiving additional AT-III (n = 230) were sicker than those on standard therapy (n = 315; admission Acute physiology and chronic health evaluation II score, 19.8 ± 7.3 vs. 17.9 ± 7.1 [mean ± SD]; P < 0.005). Correspondingly, 28-day mortality was higher in patients who had an additional AT-III therapy than in those on standard therapy (46.3% vs. 36.9%; P < 0.03), as was the number of red cell units transfused during ICU stay (21.5 ± 26.7 vs. 9.3 ± 12.1; P < 0.001). At multivariate analysis, there was no significant effect of AT-III therapy on 28-day mortality (GAM: odds ratio, 1.012; 95% confidence interval [CI], 0.651 - 1.573; P = 0.957) and 90-day survival time (Cox-type additive hazard regression: hazard ratio, 1.034; 95% CI, 0.779 - 1.387; P = 0.794). However, AT-III therapy was associated with a significantly higher frequency of red cell unit transfusion (GAM/zero-inflated Poisson: estimate, 1.26; 95% CI, 1.15 - 139; P < 0.001). Our results suggest that there seems to be no relevant effect of an activity-guided AT-III therapy on the prognosis of surgical patients with severe sepsis. However, transfusion frequency rises by AT-III therapy.
An rpsL Cassette, Janus, for Gene Replacement through Negative Selection in Streptococcus pneumoniae

ABSTRACT Natural genetic transformation offers a direct route by which synthetic gene constructs can be placed into the single circular chromosome of Streptococcus pneumoniae. However, the lack of a general negative-selection marker has hampered the introduction of constructs that do not confer a selectable phenotype. A 1.3-kb cassette was constructed comprising a kanamycin (Kn) resistance marker (kan) and a counterselectable rpsL+marker. The cassette conferred dominant streptomycin (Sm) sensitivity in an Sm-resistant background in S. pneumoniae. It was demonstrated that it could be used in a two-step transformation procedure to place DNA of arbitrary sequence at a chosen target site. The first transformation into an Sm-resistant strain used the cassette to tag a target gene on the chromosome by homologous recombination while conferring Kn resistance but Sm sensitivity on the recombinant. Replacement of the cassette by an arbitrary segment of DNA during a second transformation restored Sm resistance (and Kn sensitivity), allowing construction of silent mutations and deletions or other gene replacements which lack a selectable phenotype. It was also shown that gene conversion occurred between the two rpsL alleles in a process that depended on recA and that was susceptible to correction by mismatch repair.
The HIV-1 Subtype C Epidemic in South America Is Linked to the United Kingdom

Background The global spread of HIV-1 has been accompanied by the emergence of genetically distinct viral strains. Over the past two decades subtype C viruses, which predominate in Southern and Eastern Africa, have spread rapidly throughout parts of South America. Phylogenetic studies indicate that subtype C viruses were introduced to South America through a single founder event that occurred in Southern Brazil. However, the external route via which subtype C viruses spread to the South American continent has remained unclear. Methodology/Principal Findings We used automated genotyping to screen 8,309 HIV-1 subtype C pol gene sequences sampled within the UK for isolates genetically linked to the subtype C epidemic in South America. Maximum likelihood and Bayesian approaches were used to explore the phylogenetic relationships between 54 sequences identified in this screen, and a set of globally sampled subtype C reference sequences. Phylogenetic trees disclosed a robustly supported relationship between sequences from Brazil, the UK and East Africa. A monophyletic cluster comprised exclusively of sequences from the UK and Brazil was identified and dated to approximately the early 1980s using a Bayesian coalescent-based method. A sub-cluster of 27 sequences isolated from homosexual men of UK origin was also identified and dated to the early 1990s. Conclusions Phylogenetic, demographic and temporal data support the conclusion that the UK was a crucial staging post in the spread of subtype C from East Africa to South America. This unexpected finding demonstrates the role of diffuse international networks in the global spread of HIV-1 infection, and the utility of globally sampled viral sequence data in revealing these networks. Additionally, we show that subtype C viruses are spreading within the UK amongst men who have sex with men.
Spinal Cord Pathology in Alpha-Synuclein Transgenic Mice

Accumulation of α-synuclein is observed in neurodegenerative diseases like Parkinson's disease and Multiple System Atrophy. In previous studies with transgenic C57BL/6 mice overexpressing α-synuclein carrying the mutations A53T and A30P found in Parkinson's disease or with a parkin-null background, we reported severe mitochondrial impairments in neurons and to a larger extent in glial cells of the mesencephalon. Neuron death was not observed in the brain. Here we show that the mice show severe motor impairments in behavioral tests. In addition, these mice exhibit astrocytic cell death in the spinal cord, accompanied by extensive gliosis and microglial activation. This is shown by cell death staining and immunohistochemistry. Ultrastructural analyses revealed severe mitochondrial impairments not only in astrocytes, but also in oligodendrocytes and, to a small extent, in neurons. Thus, the transgenic mice show a profound pathology in glial cells of the spinal cord.
Structural and Biochemical Characterization Reveals LysGH15 as an Unprecedented “EF-Hand-Like” Calcium-Binding Phage Lysin

The lysin LysGH15, which is derived from the staphylococcal phage GH15, demonstrates a wide lytic spectrum and strong lytic activity against methicillin-resistant Staphylococcus aureus (MRSA). Here, we find that the lytic activity of the full-length LysGH15 and its CHAP domain is dependent on calcium ions. To elucidate the molecular mechanism, the structures of three individual domains of LysGH15 were determined. Unexpectedly, the crystal structure of the LysGH15 CHAP domain reveals an “EF-hand-like” calcium-binding site near the Cys-His-Glu-Asn quartet active site groove. To date, the calcium-binding site in the LysGH15 CHAP domain is unique among homologous proteins, and it represents the first reported calcium-binding site in the CHAP family. More importantly, the calcium ion plays an important role as a switch that modulates the CHAP domain between the active and inactive states. Structure-guided mutagenesis of the amidase-2 domain reveals that both the zinc ion and E282 are required in catalysis and enable us to propose a catalytic mechanism. Nuclear magnetic resonance (NMR) spectroscopy and titration-guided mutagenesis identify residues (e.g., N404, Y406, G407, and T408) in the SH3b domain that are involved in the interactions with the substrate. To the best of our knowledge, our results constitute the first structural information on the biochemical features of a staphylococcal phage lysin and represent a pivotal step forward in understanding this type of lysin.
Treatment of Type 2 Diabetes by Free Fatty Acid Receptor Agonists

Dietary free fatty acids (FFAs), such as ω-3 fatty acids, regulate metabolic and anti-inflammatory processes, with many of these effects attributed to FFAs interacting with a family of G protein-coupled receptors. Selective synthetic ligands for free fatty acid receptors (FFA1-4) have consequently been developed as potential treatments for type 2 diabetes (T2D). In particular, clinical studies show that Fasiglifam, an agonist of the long-chain FFA receptor, FFA1, improved glycemic control and reduced HbA1c levels in T2D patients, with a reduced risk of hypoglycemia. However, this ligand was removed from clinical trials due to potential liver toxicity and determining if this is a target or a ligand-specific feature is now of major importance. Pre-clinical studies also show that FFA4 agonism increases insulin sensitivity, induces weight loss, and reduces inflammation and the metabolic and anti-inflammatory effects of short chain fatty acids (SCFAs) are linked with FFA2 and FFA3 activation. In this review, we therefore show that FFA receptor agonism is a potential clinical target for T2D treatment and discuss ongoing drug development programs within industry and academia aimed at improving the safety and effectiveness of these potential treatments.
A Novel Sliding Window Based Change Detection Algorithm for Asymmetric Traffic

The effects of network attacks may result in abrupt changes in network traffic parameters. The speedy identification of these changes is critical for smooth network operation. This paper illustrates a sequential analysis technique for detecting these unknown abrupt changes in asymmetric network traffic. A novel sliding window based adaptive cumulative sum (CUSUM) algorithm is used to detect the cause of such variations in network traffic. The significance of the proposed algorithm is two-fold: (1) automatic adjustment of the change detection threshold while minimising the false alarm rate, and (2) timely detection of an end to the anomalous traffic. The validity of the proposed technique is investigated by experimentation on simulated data and on 18 months of real network traces collected from a class C darknet. Comparative analysis of the proposed technique with a traditional CUSUM method demonstrates its superior performance with high detection accuracy and low false alarm rate.
Two-Component System Response Regulators Involved in Virulence of Streptococcus pneumoniae TIGR4 in Infective Endocarditis

Streptococci resident in the oral cavity have been linked to infective endocarditis (IE). While other viridans streptococci are commonly studied in relation to IE, less research has been focused on Streptococcus pneumoniae. We established for the first time an animal model of S. pneumoniae IE, and examined the virulence of the TIGR4 strain in this model. We hypothesized that two-component systems (TCS) may mediate S. pneumoniae TIGR4 strain virulence in IE and examined TCS response regulator (RR) mutants of TIGR4 in vivo with the IE model. Thirteen of the 14 RR protein genes were mutagenized, excluding only the essential gene SP_1227. The requirement of the 13 RRs for S. pneumoniae competitiveness in the IE model was assessed in vivo through use of quantitative real-time PCR (qPCR) and competitive index assays. Using real-time PCR, several RR mutants were detected at significantly lower levels in infected heart valves compared with a control strain suggesting the respective RRs are candidate virulence factors for IE. The virulence reduction of the ΔciaR mutant was further confirmed by competitive index assay. Our data suggest that CiaR is a virulence factor of S. pneumoniae strain TIGR4 for IE.
The influence of morphological awareness on the literacy development of first-grade children.

PURPOSE The purpose of this study was twofold. First, we investigated whether first-grade children evidenced morphological awareness and whether they used their knowledge of morphological relations to guide their spelling. Second, we sought to determine whether children's morphological awareness abilities were predictive of their performance on word-level reading and spelling measures. METHOD At the beginning of the academic school year, 43 first-grade children were administered an oral morphological awareness production task, a series of single-word morphological spelling tasks, and a battery of language and literacy tasks. RESULTS The first-grade children were able to generate words reflecting morphological relations before they received explicit instruction regarding morphological relations between words. In addition, the children used morphological information to guide their spelling of single words, as evidenced by a difference in patterns of spellings between 1- and 2-morpheme words. Regression analyses revealed that the children's performance on the oral morphological production task explained unique variance on their reading and spelling measures above and beyond the variance that was accounted for by phonological awareness. CONCLUSION Children as young as first graders evidenced morphological awareness, and morphological awareness influenced the children's literacy development. Theoretical implications of the findings are discussed.
Physiological responses to psychological stress: importance of adiposity in men aged 50–70 years

We tested the hypothesis that overweight/obese men aged 50–70 years will have a greater salivary cortisol, salivary alpha amylase and heart rate (HR) responses to psychological stress compared with age matched lean men. Lean (BMI=20–25 kg/m2; n=19) and overweight/obese (BMI=27–35 kg/m2; n=17) men (50–70 years) were subjected to a well-characterised psychological stress (Trier Social Stress Test, TSST) at 1500 h. Concentrations of cortisol and alpha amylase were measured in saliva samples collected every 7–15 min from 1400 to 1700 h. HR was recorded using electrocardiogram. Body weight, BMI, percentage body fat, resting systolic and diastolic blood pressure and mean arterial pressure were significantly higher (P<0.05) in overweight/obese men compared with lean men. Both groups responded to the TSST with a substantial elevation in salivary cortisol (372%), salivary alpha amylase (123%) and HR (22%). These responses did not differ significantly between the groups (time×treatment interaction for salivary cortisol, salivary alpha amylase and HR; P=0.187, P=0.288, P=0.550, respectively). There were no significant differences between the groups for pretreatment values, peak height, difference between pretreatment values and peak height (reactivity) or area under the curve for salivary cortisol, salivary alpha amylase or HR (P>0.05 for all). The results showed that, for men with a moderate level of overweight/obesity who were otherwise healthy, the response of salivary cortisol, salivary alpha amylase and HR to acute psychological stress was not impaired.
Epistasis can lead to fragmented neutral spaces and contingency in evolution

In evolution, the effects of a single deleterious mutation can sometimes be compensated for by a second mutation which recovers the original phenotype. Such epistatic interactions have implications for the structure of genome space—namely, that networks of genomes encoding the same phenotype may not be connected by single mutational moves. We use the folding of RNA sequences into secondary structures as a model genotype–phenotype map and explore the neutral spaces corresponding to networks of genotypes with the same phenotype. In most of these networks, we find that it is not possible to connect all genotypes to one another by single point mutations. Instead, a network for a phenotypic structure with n bonds typically fragments into at least 2n neutral components, often of similar size. While components of the same network generate the same phenotype, they show important variations in their properties, most strikingly in their evolvability and mutational robustness. This heterogeneity implies contingency in the evolutionary process.
Modified Armstrong-Frederick Relation for Handling Back Stresses in FEM Computations

If transient phenomena are important in creep design, a non-stationary creep model must be applied. One way of achieving this is to apply a back stress. The back stress reflects the history of the creep deformation. During primary creep the back stress normally increases from zero to a stationary value representing secondary creep. A common way to derive the back stress in FEM-modelling is to use the Armstrong-Frederick relation. It is demonstrated that this can give rise to unexpected results in the sense that back stress components can be much larger than the corresponding applied stress components. Modification of the Armstrong-Frederick relation are proposed that avoid this problem. An alternative approach is also given. In this case the back stress is assumed to be a scalar. Then its value can be derived in the same way as in the uniaxial case, for example using the Bergstrom-Kocks-Mecking model for FCC alloys. In the Odqvist equation for the creep rate, the effective stress is reduced with the back stress, but the stress deviator is left unmodified. The models are applied to copper canisters for storage of nuclear waste. It is demonstrated that the models give virtually the same result.
Osmometrically Determined Characteristics of the Cell Membrane of Squid and Lobster Giant Axons

Lobster and squid giant nerve fibers respond differently when subjected to osmotic challenges. The axons proper, as distinct from the total (fiber) complex formed by the axon and connective sheath, both behave as "fast" osmometers for changes in the concentration of NaCl, but the maximum degree of swelling in hyposmotic media is by about 60% in lobster and only by 20% in squid. The relative volume intercepts of the van't Hoff relation are about 0.2 for lobster and 0.4 for squid. The sheaths of both axons undergo only small, apparently passive changes in volume. Lobster axons are permeable to Cl, but squid axons are impermeable to this anion. Lobster axons are also permeable to glycerol. The implications of the data as to the nature of volume regulation of cells are discussed.
Non-sequential decoding algorithm for hard iterative turbo product codes - [transactions letters]

In this letter, we propose a new decoding algorithm to improve the bit error rate performance of the hard-input hard-output (HIHO) turbo product codes (TPC) with hard iterative decoding. The proposed algorithm iteratively, but not sequentially, decodes the received TPC blocks based on the reliability of the constituent codes. Simulation results confirm a noticeable coding gain improvement using the proposed decoding process with respect to standard HIHO TPC decoding. An efficient implementation of the new technique offers a negligible additional complexity when the channel-bit error probability is less than 10-2.
Using chlorophyll meter readings to determine N application rates for corn

One method for refining nitrogen (N) application in corn is use of in-season crop sensing. To aid producers in making decisions regarding N rate adjustments, a calibrated relationship between sensor-derived information and expected N application need should be established. Nitrogen rate trials were conducted at multiple sites across Iowa in 2001-2003. Nitrogen was applied at or shortly after corn planting. Minolta SPAD chlorophyll meter (CM) readings were collected at the R1 growth stage from the ear leaf. The results show a statistically significant quadratic-plateau relationship between relative chlorophyll meter (RCM) values and differential from economic optimum N rate (R 2 = 0.69, P < 0.001). The regression fit resulted in a 0.97 RCM value at zero differential from economic optimum N. A related study in 2003 at six N rate by crop rotation sites showed RCM values at the V15 and R1 growth stages were similar. This indicates adequate time is available to collect readings after significant corn N uptake and before making in-season N adjustments. This relationship between RCM value and differential from economic optimum N rate could be used by producers to determine additional N need.