Miracle-dz/UniFAR-FTUs huggingface dataset:
On global sequence alignment

We present a dynamic programming algorithm for computing a best global alignment of two sequences. The proposed algorithm is robust in identifying any of several global relationships between two sequences. The algorithm delivers a best alignment of two sequences in linear space and quadratic time. We also describe a multiple alignment algorithm based on the pairwise algorithm. Both algorithms have been implemented as portable C programs. Experimental results indicate that for a commonly used set of gap penalties, the new programs produce more satisfactory alignments on sequences of various lengths than some existing pairwise and multiple programs based on the dynamic programming algorithm of Needleman and Wunsch.
Neurosurgeons address EC/IC study; question controlled surgical trials.

LAST YEAR, Sydney J. Peerless, MD, was among the first to learn the results of an eight-year international surgical study. "My jaw dropped. I couldn't believe what I found," he said. "What the data were telling me was that with 95% confidence we can rule out a 5% benefit from extracranial/intracranial [EC/IC] bypass surgery. " Peerless, who is professor of neurosurgery at Canada's University of Western Ontario, London, was principal neurosurgical investigator in the 71-center study. His incredulity was mirrored 500-fold when the study was presented at the International Congress of Neurosurgery in Toronto a month later. And, when he reprised the study's findings at a special symposium at the American Association of Neurological Surgeons in Denver this spring, it was apparent that many of his colleagues still refused to believe what they were hearing. Yet the message was straightforward. The neurosurgeons were told that the intricate microsurgical procedure—the anastamosis of
A role for 12/15‐lipoxygenase‐derived proresolving mediators in postoperative ileus: protectin DX‐regulated neutrophil extravasation

Resolution of inflammation is an active counter‐regulatory mechanism involving polyunsaturated fatty acid‐derived proresolving lipid mediators. Postoperative intestinal motility disturbances, clinically known as postoperative ileus, occur frequently after abdominal surgery and are mediated by a complex inflammation of the intestinal muscularis externa. Herein, we tested the hypothesis that proresolving lipid mediators are involved in the resolution of postoperative ileus. In a standardized experimental model of postoperative ileus, we detected strong expression of 12/15‐lipoxygenase within the postoperative muscularis externa of C57BL/6 mice, predominately located within CX3CR1+/Ly6C+ infiltrating monocytes rather than Ly6G+ neutrophils. Mass spectrometry analyses demonstrated that a 12/15‐lipoxygenase increase was accompanied by production of docosahexaenoic acid‐derived lipid mediators, particularly protectin DX and resolvin D2, and their common precursor 17‐hydroxy docosahexaenoic acid. Perioperative administration of protectin DX, but not resolvin D2 diminished blood‐derived leukocyte infiltration into the surgically manipulated muscularis externa and improved the gastrointestinal motility. Flow cytometry analyses showed impaired Ly6G+/Ly6C+ neutrophil extravasation after protectin DX treatment, whereas Ly6G‐/Ly6C+ monocyte numbers were not affected. 12/15‐lipoxygenase‐deficient mice, lacking endogenous protectin DX synthesis, demonstrated increased postoperative leukocyte levels. Preoperative intravenous administration of a docosahexaenoic acid‐rich lipid emulsion reduced postoperative leukocyte infiltration in wild‐type mice but failed in 12/15‐lipoxygenase‐deficient mice mice. Protectin DX application reduced leukocyte influx and rescued 12/15‐lipoxygenase‐deficient mice mice from postoperative ileus. In conclusion, our results show that 12/15‐lipoxygenase mediates postoperative ileus resolution via production of proresolving docosahexaenoic acid‐derived protectin DX. Perioperative, parenteral protectin DX or docosahexaenoic acid supplementation, as well as modulation of the 12/15‐lipoxygenase pathway, may be instrumental in prevention of postoperative ileus.
Direct Evidence of Reassortment and Mutant Spectrum Analysis of a Very Virulent Infectious Bursal Disease Virus

Abstract The complete genomic sequence of very virulent infectious bursal disease virus (vvIBDV) Gx strain was determined, including the sequences of segment A, encoding the precursor polyprotein, and segment B, encoding the viral RNA polymerase (VP1) and 5′- and 3′-untranslating regions. Alignment of segment A of Gx with the sequences of 12 other vvIBDV strains showed 97.5% to 99.0% amino acid identity, whereas alignment of segment B of Gx with nine other vvIBDV strains revealed high sequence divergence, ranging from 10.3% to 11%. Phylogenetic analysis of segments A and B showed that they were in different branches, indicating that the reassortment occurred in this strain and that segment A and segment B derived from different pathotype strains. The mutant spectrum analysis of quasispecies virus demonstrated that the mean minimum mutation frequency in VP1 was 8.78-fold higher than in the polyprotein. The most frequent mutations were in the first 1986 nucleotides (nonsynonymous mutations) and the last 660 nucleotides (synonymous mutations), indicating that the 219 amino acid residues in the C-terminal of the VP1 form a functional region.
An Analysis of Surgical Treatment for the Spontaneous Rupture of Hepatocellular Carcinoma

Background/Aims: The prognosis of spontaneous rupture of hepatocellular carcinoma (HCC) remains unclear. We investigated the prognosis of patients with ruptured HCC based on the treatments and prognostic factors associated with long-term survival. Methods: The prognoses of 64 consecutive patients treated for ruptured HCC from 1986 to 2013 were analyzed according to their methods of treatment. The prognostic factors of 16 surgical patients were identified, and their overall survival (OS) and recurrence rates were compared to 1,157 surgical patients who underwent surgery for non-ruptured HCC. The surgical outcomes were also compared using a propensity score matching method. Results: Surgery was associated with a better OS. Curative resection was the only independent prognostic factor in surgical patients with ruptured HCC (p = 0.040). Although the OS of surgical patients with non-ruptured HCC was found to be significantly better than that of the patients with ruptured HCC, no significant difference in OS was observed after propensity score matching. Conclusion: A curative resection should be the objective of treatment, assuming the suitability of the patient's clinical condition. When the liver function reserve and tumor extension of patients with ruptured and non-ruptured HCC are similar, then their surgical outcomes may not be significantly different.
Anal Incontinence Improvement After Silicone Injection May Be Related to Restoration of Sphincter Asymmetry

Background. This study aimed to evaluate manometric parameters that may explain improvement in anal incontinence using a silicone bulking agent. Methods. Incontinent patients having internal sphincter defects were prospectively selected and injected with a silicone bulking agent. Manometry and endoanal ultrasound were performed before and 3 months after injections. Twenty continent healthy volunteers were used only for manometric comparison. Results. Thirty-five patients (28 females; mean age 60.3 years) and 20 controls entered this study. Patients had lower resting and squeeze pressures compared with controls (P < .05). Length of the high-pressure zone increased from 1 to 1.7 cm postinjection (P = .002). Asymmetry index showed a significant change postinjection (P < .001). Conclusion. Despite considerable clinical improvement, no significant increase in manometric pressures was noted posttreatment. There was significant improvement in both high-pressure zone and asymmetry index, and these findings may explain the mechanism of action of the bulking agent injected.
Role conflict, work-family conflict and job satisfaction among single mother employees.

Despite previous studies on job satisfaction and its antecedents, few studies have explored the interrelationships between role conflict, work-family conflict and job satisfaction. The purpose of this study is to determine the effect of role conflict on job satisfaction, with work-family conflict as a potential mediator. Data were gathered from 159 Malaysian single mother employees, aged 45 and below, using self-administered questionnaires. Results of regression analyses indicate that work-family conflict serves as one of the mechanisms through which role conflict influences job satisfaction. Role conflict experienced at the workplace can increase the interrole conflict between work and family domains which in turn can reduce the level of job satisfaction. The findings suggest that to improve the job satisfaction of employees the management should avoid seeing the problem of work in isolation from the total life space of employees.
Physical Therapy and Splinting After Flexor Tendon Repair in Zone II

ABSTRACT Introduction: Early physical therapy and splinting after flexor tendon repair in zone II is very important to improve tendon healing, increase tensile strength, decrease adhesion formation, early return of function and less stiffness and deformity. We conducted a study to observe and record the results of early active mobilization of repaired flexor tendons in zone II. Materials and method: This study reports the results of physical therapy and splinting which was applied to 75 patients with 76 digits after flexor tendon repair in zone II, treated at the Department of Plastic Surgery and Physical and Rehabilitation Medicine Clinic, Pristine-Kosovo. Physical therapy and splinting started the first day after surgery and have lasts until week 12. Patients were evaluated with regarding to the range of motion and grip strength. The assessments were done at the 8, 10, 12 weeks and the finale assessments were done after 6 months. Results: Range of motion after 6 months according to the Strickland Classification were excellent in 21.1%, good in 44.7%, fair in 11.8% and poor in 22.4%. Grip strength was good in 63.8% of cases. Conclusion: Results of this study shows that using a physical therapy and splinting achieve good results in range of motion, muscle force and early return of function of the hand.
The ASYMMETRIC LEAVES Complex Employs Multiple Modes of Regulation to Affect Adaxial-Abaxial Patterning and Leaf Complexity[OPEN]

Using diverse mechanisms of regulation at MIR166A, YAB5, ARF3, and TAS3A, AS1-AS2 affects adaxial-abaxial polarity and leaf complexity to keep the leaf both flat and simple. Flattened leaf architecture is not a default state but depends on positional information to precisely coordinate patterns of cell division in the growing primordium. This information is provided, in part, by the boundary between the adaxial (top) and abaxial (bottom) domains of the leaf, which are specified via an intricate gene regulatory network whose precise circuitry remains poorly defined. Here, we examined the contribution of the ASYMMETRIC LEAVES (AS) pathway to adaxial-abaxial patterning in Arabidopsis thaliana and demonstrate that AS1-AS2 affects this process via multiple, distinct regulatory mechanisms. AS1-AS2 uses Polycomb-dependent and -independent mechanisms to directly repress the abaxial determinants MIR166A, YABBY5, and AUXIN RESPONSE FACTOR3 (ARF3), as well as a nonrepressive mechanism in the regulation of the adaxial determinant TAS3A. These regulatory interactions, together with data from prior studies, lead to a model in which the sequential polarization of determinants, including AS1-AS2, explains the establishment and maintenance of adaxial-abaxial leaf polarity. Moreover, our analyses show that the shared repression of ARF3 by the AS and trans-acting small interfering RNA (ta-siRNA) pathways intersects with additional AS1-AS2 targets to affect multiple nodes in leaf development, impacting polarity as well as leaf complexity. These data illustrate the surprisingly multifaceted contribution of AS1-AS2 to leaf development showing that, in conjunction with the ta-siRNA pathway, AS1-AS2 keeps the Arabidopsis leaf both flat and simple.
The Impact of Board Size, CEO Duality, and Corporate Liquidity on the Profitability of Canadian Service Firms

The purpose of this study is to examine the impact of board size, the CEO (Chief Executive Officer) duality, and corporate liquidity on the profitability of Canadian service firms. This study also seeks to extend the findings of Kajola [1] and Gill [2]. A sample of 75 Canadian service firms listed on Toronto Stock Exchange (TSX) for a period of 3 years (from 2008-2010) was selected. This study applied co-relational and non-experimental research design. The results indicate that larger board size (large number of directors) negatively impact on the profitability of Canadian service firms. The findings of this paper also show that the CEO duality and corporate liquidity positively impact the profitability of Canadian service firms. In addition, firm size and firm growth positively impact the profitability of Canadian service firms. This study contributes to the literature on the factors that affect firmâ€™s profitability. The findings may be useful for the financial managers, investors, and financial management consultants.
Anthropometry Increases 1 Repetition Maximum Predictive Ability of NFL-225 Test for Division IA College Football Players

Hetzler, RK, Schroeder, BL, Wages, JJ, Stickley, CD, and Kimura, IF. Anthropometry increases 1 repetition maximum predictive ability of NFL-225 test for division IA college football players. J Strength Cond Res 24(6): 1429-1439, 2010-The purpose of this study was to compare existing 1 repetition maximum (1RM) bench press prediction equations in National Collegiate Athletic Association (NCAA) Division IA college football players and determine if the error associated with the prediction of 1RM bench press from the National Football League (NFL)-225 test could be reduced through the addition of anthropometric measurements. Anthropometric measures, 1RM bench press, NFL-225 test repetitions to fatigue, and body composition data were collected on 87 Division IA football players (mean ± SD age 19.9 ± 1.3 years; height 182.3 ± 7.3 cm; body mass 102.3 ± 21.1 kg; % fat 13.9 ± 6.7; 1RM bench press 140.5 ± 2 6.6 kg; and NFL-225 reps to fatigue 14.1 ± 8.0). Hierarchical regression revealed an R2 = 0.87 when predicting 1RM from the NFL-225 test alone, which improved to R2 = 0.90 with the addition of the anthropometric variables: arm circumference and arm length. The following equation was the best performing model to predict 1RM bench press: 1RM (lb) = 299.08 + 2.47 arm circumference (cm) − 4.60 arm length (cm) + 5.84 reps @ 225; SEE = 18.3 lb). This equation predicted 43.7% of subjects' within ±10 lb of their actual 1RM bench press. Using a crossvalidation group, the equation resulted in estimates of 1RM which were not significantly different than the actual 1RM. Because of the variability that has been shown to be associated with 1RM prediction equations, the use of actual 1RM testing is recommended when this is a critical variable. However, coaches, scouts, and athletes, who choose to estimate 1RM bench press using repetitions to failure from the NFL-225 test, may benefit from the use of the equations developed in this study to estimate 1RM bench press with the inclusion of simple anthropometric measurements.
Expression of transforming growth factor beta(1), beta(3), and basic fibroblast growth factor in full-thickness skin wounds of equine limbs and thorax.

OBJECTIVE To map the expression of transforming growth factor (TGF)-beta(1), TGF-beta(3), and basic fibroblast growth factor (bFGF) in full-thickness skin wounds of the horse. To determine whether their expression differs between limbs and thorax, to understand the pathogenesis of exuberant granulation tissue. STUDY DESIGN Six wounds were created on one lateral metacarpal area and one midthoracic area of each horse. Sequential wound biopsies allowed comparison of the temporal expression of growth factors between limb and thoracic wounds. ANIMALS Four 2- to 4-year-old horses. METHODS Wounds were assessed grossly and histologically at 12 and 24 hours, and 2, 5, 10, and 14 days postoperatively. ELISAs were used to measure the growth factor concentrations of homogenates of wound biopsies taken at the same timepoints. RESULTS TGF-beta(1) peaked at 24 hours in both locations and returned to baseline in thoracic wounds by 14 days but remained elevated in limb wounds for the duration of the study. Expression kinetics of TGF-beta(3) differed from those of TGF-beta(1). TGF-beta(3) concentrations gradually increased over time, showing a trend toward an earlier and higher peak in thoracic compared with limb wounds. bFGF expression kinetics resembled those of TGF-beta(1), but no statistically significant differences existed between limb and thoracic wounds. CONCLUSIONS Growth factor expression is up-regulated during normal equine wound repair. TGF-beta(1) and TGF-beta(3) show a reciprocal temporal regulation. Statistically significant differences exist between limb and thoracic wounds with respect to TGF-beta(1) expression. CLINICAL RELEVANCE The persistence of TGF-beta(1) expression in leg wounds may be related to the development of exuberant granulation tissue in this location, because TGF-beta(1) is profibrotic.
Strain Level Streptococcus Colonization Patterns during the First Year of Life

Pneumococcal pneumonia has decreased significantly since the implementation of the pneumococcal conjugate vaccine (PCV), nevertheless, in many developing countries pneumonia mortality in infants remains high. We have undertaken a study of the nasopharyngeal (NP) microbiome during the first year of life in infants from The Philippines and South Africa. The study entailed the determination of the Streptococcus sp. carriage using a lytA qPCR assay, whole metagenomic sequencing, and in silico serotyping of Streptococcus pneumoniae, as well as 16S rRNA amplicon based community profiling. The lytA carriage in both populations increased with infant age and lytA+ samples ranged from 24 to 85% of the samples at each sampling time point. We next developed informatic tools for determining Streptococcus community composition and pneumococcal serotype from metagenomic sequences derived from a subset of longitudinal lytA-positive Streptococcus enrichment cultures from The Philippines (n = 26 infants, 50% vaccinated) and South African (n = 7 infants, 100% vaccinated). NP samples from infants were passaged in enrichment media, and metagenomic DNA was purified and sequenced. In silico capsular serotyping of these 51 metagenomic assemblies assigned known serotypes in 28 samples, and the co-occurrence of serotypes in 5 samples. Eighteen samples were not typeable using known serotypes but did encode for capsule biosynthetic cluster genes similar to non-encapsulated reference sequences. In addition, we performed metagenomic assembly and 16S rRNA amplicon profiling to understand co-colonization dynamics of Streptococcus sp. and other NP genera, revealing the presence of multiple Streptococcus species as well as potential respiratory pathogens in healthy infants. A range of virulence and drug resistant elements were identified as circulating in the NP microbiomes of these infants. This study revealed the frequent co-occurrence of multiple S. pneumoniae strains along with Streptococcus sp. and other potential pathogens such as S. aureus in the NP microbiome of these infants. In addition, the in silico serotype analysis proved powerful in determining the serotypes in S. pneumoniae carriage, and may lead to developing better targeted vaccines to prevent invasive pneumococcal disease (IPD) in these countries. These findings suggest that NP colonization by S. pneumoniae during the first years of life is a dynamic process involving multiple serotypes and species.
Recovery from Unrecognized Sleep Loss Accumulated in Daily Life Improved Mood Regulation via Prefrontal Suppression of Amygdala Activity

Many modern people suffer from sleep debt that has accumulated in everyday life but is not subjectively noticed [potential sleep debt (PSD)]. Our hypothesis for this study was that resolution of PSD through sleep extension optimizes mood regulation by altering the functional connectivity between the amygdala and prefrontal cortex. Fifteen healthy male participants underwent an experiment consisting of a baseline (BL) evaluation followed by two successive interventions, namely, a 9-day sleep extension followed by one night of total sleep deprivation (TSD). Tests performed before and after the interventions included a questionnaire on negative mood and neuroimaging with arterial spin labeling MRI for evaluating regional cerebral blood flow (rCBF) and functional connectivity. Negative mood and amygdala rCBF were significantly reduced after sleep extension compared with BL. The amygdala had a significant negative functional connectivity with the medial prefrontal cortex (FCamg–MPFC), and this negative connectivity was greater after sleep extension than at BL. After TSD, these indices reverted to the same level as at BL. An additional path analysis with structural equation modeling showed that the FCamg–MPFC significantly explained the amygdala rCBF and that the amygdala rCBF significantly explained the negative mood. These findings suggest that the use of our sleep extension protocol normalized amygdala activity via negative amygdala–MPFC functional connectivity. The resolution of unnoticed PSD may improve mood by enhancing frontal suppression of hyperactivity in the amygdala caused by PSD accumulating in everyday life.
Comparison of lateral versus triceps-splitting posterior approach in the surgical treatment of pediatric supracondylar humerus fractures.

BACKGROUND Supracondylar humerus fracture is the most common fracture of the elbow in children. Closed reduction and percutaneous pinning is considered to be the optimal treatment strategy; however, in some instances, open reduction may be necessary. The aim of this retrospective study was to compare clinical and functional results of triceps-splitting posterior versus lateral approach in pediatric supracondylar humerus fracture surgery. METHODS A total of 38 patients underwent surgery; Group 1 consisted of 30 patients on whom posterior approach was used, while lateral approach was used on the 8 patients in Group 2. Flynn criteria were used to evaluate cosmetic and clinical results. Fracture healing was assessed with anteroposterior and lateral x-rays. Patients and parents were asked to describe time needed for complete return of full elbow range of motion (ROM) and overall satisfaction. RESULTS Mean fracture union time was 44.1 days and 46.3 days, and time required to regain complete or near complete elbow ROM was 57.5 days and 55.7 days after splint removal for Group 1 and Group 2, respectively. Twenty-one of 30 (70%) patients (and parents) in Group 1, and 6 of 8 (75%) patients (and parents) in Group 2 were totally satisfied with the results. Twenty-one of 30 (70%) patients in Group 1, and 6 of 8 (75%) patients in Group 2 had excellent cosmetic and functional results according to Flynn outcome criteria. CONCLUSION In cases of pediatric supracondylar humerus fracture, early closed reduction and percutaneous pinning is preferred; however, when this method is not applicable, triceps-splitting posterior approach is a safe and comparable method to lateral approach with advantages of easier fracture reduction and shorter operating time.