Miracle-dz/UniFAR-FTUs huggingface dataset:
Intramuscular nerve damage in lacerated skeletal muscles may direct the inflammatory cytokine response during recovery

The expression of inflammatory cytokines and growth factors in surgically repaired lacerated muscles over a 12‐week recovery phase was investigated. We hypothesized that these expression levels are influenced by both neural and muscular damage within lacerated muscles. Microarrays were confirmed with reverse transcription‐polymerase chain reaction assays and histology of biopsies at the lesion of three simulated lacerated muscle models in 130 adult rats. The lacerated medial gastrocnemius with the main intramuscular nerve branch either cut (DN), crushed but leaving an intact nerve sheath (RN); or preserved intact (PN) were compared. At 4 weeks, DN had a higher number of interleukins up‐regulated. DN and RN also had a set of Bmp genes significantly expressed between 2 and 8 weeks (P ≤ 0.05). By 12 weeks, DN had a poorer and slower myogenic recovery and greater fibrosis formation correlating with an up‐regulation of the Tgf‐β gene family. DN also showed poorer re‐innervation with higher mRNA expression levels of nerve growth factor (Ngf) and brain‐derived neurotrophin growth factor (Bdnf) over RN and PN. This study demonstrates that the inflammatory response over 12 weeks in lacerated muscles may be directed by the type of intramuscular nerve damage, which can influence the recovery at the lesion site. Inflammatory‐related genes associated to the type of intramuscular nerve damage include Gas‐6, Artemin, Fgf10, Gdf8, Cntf, Lif, and Igf‐2. qPCR also found up‐regulation of Bdnf (1‐week), neurotrophin‐3 (2w), Lif (4w), and Ngf (4w, 8w) mRNA expressions in DN, making them possible candidates for therapeutic treatment to arrest the poor recovery in muscle lacerations (250). J. Cell. Biochem. 113: 2330–2345, 2012. © 2012 Wiley Periodicals, Inc.
Biased discordance of KRAS mutation detection in archived colorectal cancer specimens between the ARMS-Scorpion method and direct sequencing.

OBJECTIVE The concordance of KRAS mutation detection between the amplification refractory mutation system-Scorpion assay and direct sequencing was evaluated with clinically available formalin-fixed, paraffin-embedded specimens of metastatic colorectal cancers. METHODS Genomic DNA from 120 macrodissected specimens was examined by the amplification refractory mutation system-Scorpion assay and direct sequencing. DNA mixtures of wild-type and mutant KRAS genes were prepared from the peripheral blood and the SW620 human colon cancer cell line for the model experiments. RESULTS KRAS mutation was identified in 50 samples (41.7%) by the amplification refractory mutation system-Scorpion assay and 42 samples (35.0%) by direct sequencing. Discordance between the two methods was observed for samples with smaller amounts of amplifiable DNA. The sensitivity of direct sequencing was impaired by the decrease in template DNA and polymerase chain reaction cycles in the experimental models. CONCLUSIONS Decreased sensitivity of direct sequencing caused by insufficient polymerase chain reaction amplification resulted in biased discordance between direct sequencing and amplification refractory mutation system-Scorpion. Polymerase chain reaction conditions satisfactory for amplifying tens of haploid copies of genomic DNA to the saturation level might be necessary to ensure the robustness of the direct sequencing-based method employed for formalin-fixed, paraffin-embedded specimen-derived DNA samples.
Variation in the postpartum hemorrhage rate in a clinical trial of oral misoprostol

Objective. The main objective of this study was to identify factors associated with variation in the rate of acute postpartum hemorrhage (PPH), defined as blood loss ≥ 500 mL within 2 hours of delivery, observed in a randomized clinical trial of misoprostol for the prevention of PPH, conducted in rural India. Although the women in the misoprostol group had a significantly lower probability of having a PPH, we also noted a reduction in the rate of PPH in the placebo group over the course of the study. We hypothesized that this was due to the changing skills of the auxiliary nurse midwives (ANMs) over the course of the study. Methods. We conducted a post-hoc analysis examining variation in PPH rates over the duration of the trial among the women randomized to the placebo arm (n = 808). Descriptive, correlation analysis and generalized estimating equations (GEE) were used to predict PPH rates. With no direct measure of ANM skills, we used proxy measures, including: (1) the ANM's point of entry into the study (original ANMs at the initiation of the trial were less skilled than replacement ANMs); (2) the study duration, representing exposure of the ANM to ongoing training and monitoring; and (3) duration of the second stage of labor as a measure of improved delivery practices. Results. As the study duration increased, the duration of the second stage of labor decreased (−0.12, p = 0.001) and as the duration of the second stage of labor decreased, the rate of PPH decreased (0.0282; 95% CI 0.0201–0.0363). For each 10-minute increase in the duration of second stage labor increased PPH odds by 7.1% and each 30-day duration of the trial decreased PPH odds by 3.4%. Additionally, a patient delivered by an original ANM was 3.14 times more likely to have a PPH compared to a patient delivered by a replacement ANM. Conclusions. Declining PPH rates were associated with improved skills and delivery practices that decreased duration of the second stage of labor. These improvements appeared to be consistent with the introduction of the more skilled replacement ANMs as well as ongoing training and monitoring for all ANMs over the duration of the trial.
Relevance feedback and inference networks

Relevance feedback, which modifies queries using judgements of the relevance of a few, highly-ranked documents, has historically been an important method for increasing the performance of information retrieval systems. In this paper, we extend the inference network model introduced by Turtle and Croft to include relevance feedback techniques. The difference between relevance feedback on text abstracts and full text collections is studied. Preliminary results for relevance feedback on the structured queries supported by the inference net model are also reported.
Short-Term Radiographic Analysis of Operative Correction of Adult Acquired Flatfoot Deformity

Background: Multiple procedures have been described to treat stage II (flexible) deformities driven by the clinical presence of “mild” versus “severe” deformity. The purpose of this study was to identify the radiographic correction after bony realignment procedures and to compare preoperative measures with postoperative measures to better understand the clinical application of these procedures. Methods: Seventy-two feet in 68 patients treated for stage II deformity between January 1999 and December 2010 were available for retrospective chart review. The average age of the patients was 55 years, and final radiographs were evaluated at an average of 9 months postoperatively. All patients had a flexor digitorum longus transfer to the navicular and bony realignment. Radiographic parameters measured included lateral talus-first metatarsal angle, medial cuneiform-floor distance, calcaneal pitch, anteroposterior talus-second metatarsal angle, and talonavicular coverage angle. Differences in pre- and postoperative measurements and between group comparisons were analyzed. Results: Three patient groups were identified: medial displacement calcaneal osteotomy (group 1), lateral column lengthening (group 2), and both medial displacement calcaneal osteotomy and lateral column lengthening (group 3). The lateral talus-first metatarsal angle mean difference was 5.1 degrees in group 1, 16.2 degrees in group 2, and 16.5 degrees in group 3. The talonavicular coverage angle mean difference was 5.7 degrees in group 1, 24.2 degrees in group 2, and 19.4 degrees in group 3. Changes in pre- to postoperative measures were statistically significant for all groups for the parameters measured. The pairwise group comparison revealed a statistically significant difference in the correction obtained in group 3 compared with that of group 1. Conclusion: Clinical and radiographic parameters are a consideration when choosing bony realignment procedures to reconstruct a flexible flatfoot deformity. In the treatment of more severe deformities, lateral column lengthening resulted in a greater radiographic improvement in alignment. A medial displacement osteotomy alone is also a valuable tool to correct these deformities although it provided a different level of correction compared with the lateral column lengthening. Level of Evidence: Level III, comparative case series.
Optimizing rice yields while minimizing yield‐scaled global warming potential

To meet growing global food demand with limited land and reduced environmental impact, agricultural greenhouse gas (GHG) emissions are increasingly evaluated with respect to crop productivity, i.e., on a yield‐scaled as opposed to area basis. Here, we compiled available field data on CH4 and N2O emissions from rice production systems to test the hypothesis that in response to fertilizer nitrogen (N) addition, yield‐scaled global warming potential (GWP) will be minimized at N rates that maximize yields. Within each study, yield N surplus was calculated to estimate deficit or excess N application rates with respect to the optimal N rate (defined as the N rate at which maximum yield was achieved). Relationships between yield N surplus and GHG emissions were assessed using linear and nonlinear mixed‐effects models. Results indicate that yields increased in response to increasing N surplus when moving from deficit to optimal N rates. At N rates contributing to a yield N surplus, N2O and yield‐scaled N2O emissions increased exponentially. In contrast, CH4 emissions were not impacted by N inputs. Accordingly, yield‐scaled CH4 emissions decreased with N addition. Overall, yield‐scaled GWP was minimized at optimal N rates, decreasing by 21% compared to treatments without N addition. These results are unique compared to aerobic cropping systems in which N2O emissions are the primary contributor to GWP, meaning yield‐scaled GWP may not necessarily decrease for aerobic crops when yields are optimized by N fertilizer addition. Balancing gains in agricultural productivity with climate change concerns, this work supports the concept that high rice yields can be achieved with minimal yield‐scaled GWP through optimal N application rates. Moreover, additional improvements in N use efficiency may further reduce yield‐scaled GWP, thereby strengthening the economic and environmental sustainability of rice systems.
Structure and dynamics of the force-generating domain of myosin probed by multifrequency electron paramagnetic resonance.

Spin-labeling and multifrequency EPR spectroscopy were used to probe the dynamic local structure of skeletal myosin in the region of force generation. Subfragment 1 (S1) of rabbit skeletal myosin was labeled with an iodoacetamide spin label at C707 (SH1). X- and W-band EPR spectra were recorded for the apo state and in the presence of ADP and nucleotide analogs. EPR spectra were analyzed in terms of spin-label rotational motion within myosin by fitting them with simulated spectra. Two models were considered: rapid-limit oscillation (spectrum-dependent on the orientational distribution only) and slow restricted motion (spectrum-dependent on the rotational correlation time and the orientational distribution). The global analysis of spectra obtained at two microwave frequencies (9.4 GHz and 94 GHz) produced clear support for the second model and enabled detailed determination of rates and amplitudes of rotational motion and resolution of multiple conformational states. The apo biochemical state is well-described by a single structural state of myosin (M) with very restricted slow motion of the spin label. The ADP-bound biochemical state of myosin also reveals a single structural state (M*, shown previously to be the same as the post-powerstroke ATP-bound state), with less restricted slow motion of the spin label. In contrast, the extra resolution available at 94 GHz reveals that the EPR spectrum of the S1.ADP. V(i)-bound biochemical state of myosin, which presumably mimics the S1.ADP. P(i) state, is resolved clearly into three spectral components (structural states). One state is indistinguishable from that of the ADP-bound state (M*) and is characterized by moderate restriction and slow motion, with a mole fraction of 16%. The remaining 84% (M**) contains two additional components and is characterized by fast rotation about the x axis of the spin label. After analyzing EPR spectra, myosin ATPase activity, and available structural information for myosin II, we conclude that post-powerstroke and pre-powerstroke structural states (M* and M**) coexist in the S1.ADP. V(i) biochemical state. We propose that the pre-powerstroke state M** is characterized by two structural states that could reflect flexibility between the converter and N-terminal domains of myosin.
Somatoform and dissociative disorders in children and adolescents: A comparative study

Background: Somatoform and dissociative (conversion) disorders in adults have been reported to have a close relationship because of a diagnostic overlap and comparable aetiological models. The literature on these disorders in children and adolescents is scarce. Aim: The present study attempted to compare these two disorders in children and adolescents since antecedents of these disorders are said to be laid in childhood. Methods: Case files of 118 patients (69 of somatoform disorders and 49 of dissociative disorders) were reviewed and the two groups were compared with respect to sociodemographic profile, clinical profile, neurotic traits, behavioural problems, temperament, intelligence and family dysfunction. Results: Age at presentation and intelligence were significantly higher in those with somatoform disorders than in those with dissociative disorders. Patients with dissociative disorders had a significantly higher number of co-morbid somatoform symptoms. Conclusion: Somatoform and dissociative disorders are closely linked.
Transfusion‐related acute lung injury: three decades of progress but miles to go before we sleep

T he year 2015 marks the 30th anniversary of the original characterization of transfusion-related acute lung injury (TRALI). The investigators at the Mayo Clinic gave form and substance to what physicians had previously observed—that transfusion can act as the trigger for life-threatening acute respiratory distress. In the 1950s and 1960s others had used such descriptors as allergic pulmonary edema, pulmonary hypersensitivity, leukoagglutinin transfusion reaction, and noncardiogenic pulmonary edema, reflecting a poorly understood picture of what was believed to be a rare phenomenon. By identifying TRALI as a syndrome and establishing the importance of passive transfusion of HLA and HNA antibodies, the early work of Popovsky and colleagues became the basis of subsequent research and efforts for mitigation and prevention. Now, three decades later, much satisfaction can be gleaned from what has been accomplished. However, key questions remain:
Aging and HIV-related cognitive loss.

LTHOUGH ANTIRETROVIRAL THERAPY HAS HAD A MAjor effect on improving the survival of individuals with human immunodeficiency virus (HIV), cognitive disorders related to HIV remain an important burden of disease and disability worldwide. Among the more than 30 million adults living with HIV worldwide,asubstantialproportionisestimatedtohavesomeform of HIV-associated neurocognitive disorders encompassing HIVdementia,mildneurocognitiveimpairment,andasymptomatic neurocognitive impairment. 1 Conservative estimatesfrombetterresourcedcountriessuggestthatthenumberofindividualsofallageslivingwithHIV-relatedcognitive disorderswillincrease5-to10-foldby2030. 2 Althoughdata from Africa are sparse, 30% of the HIV-infected population in 1 Ugandan outpatient clinic experienced some form of HIV-associated cognitive loss. 3
An ISOCAM survey through gravitationally lensing galaxy clusters IV. Luminous infrared galaxies in Cl 0024+1654 and the dynamical status of clusters

Observations of the core of the massive cluster Cl 0024+1654, at a redshift z=0.39, were obtained with the Infrared Space Observatory using ISOCAM at 6.7 mum and 14.3 mum (hereafter 15 mum). Thirty five sources were detected at 15 mum and thirteen of them are spectroscopically identified with cluster galaxies. The remaining sources consist of four stars, one quasar, one foreground galaxy, three background galaxies and thirteen sources with unknown redshift. The ISOCAM sources have best-fit SEDs typical of spiral or starburst models observed 1 Gyr after the main starburst event. The median infrared luminosity of the twelve cluster galaxies is 1.0x10^11 Lsun, with 10 having infrared luminosity above 9x10^10 Lsun, and so lying near or above the 1x10^11 Lsun threshold for identification as a luminous infrared galaxy (LIRG). The [OII] star formation rates obtained for 3 cluster galaxies are one to two orders of magnitude lower than the infrared values, implying that most of the star formation is missed in the optical because it is enshrouded by dust in the starburst galaxy. The counterparts of about half of the 15 mum cluster sources are blue, luminous, star-forming systems and the type of galaxy that is usually associated with the Butcher-Oemler effect. Dust obscuration may be a major cause of the 15 mum sources appearing on the cluster main sequence. The majority of the ISOCAM sources in the Butcher-Oemler region of the colour-magnitude diagram are best fit by spiral-type SEDs whereas post-starburst models are preferred on the main sequence, with the starburst event probably triggered by interaction with one or more galaxies. Finally, the mid-infrared results on Cl 0024+1654 are compared with four other clusters observed with ISOCAM.
Cognitive spare capacity in older adults with hearing loss

Individual differences in working memory capacity (WMC) are associated with speech recognition in adverse conditions, reflecting the need to maintain and process speech fragments until lexical access can be achieved. When working memory resources are engaged in unlocking the lexicon, there is less Cognitive Spare Capacity (CSC) available for higher level processing of speech. CSC is essential for interpreting the linguistic content of speech input and preparing an appropriate response, that is, engaging in conversation. Previously, we showed, using a Cognitive Spare Capacity Test (CSCT) that in young adults with normal hearing, CSC was not generally related to WMC and that when CSC decreased in noise it could be restored by visual cues. In the present study, we investigated CSC in 24 older adults with age-related hearing loss, by administering the CSCT and a battery of cognitive tests. We found generally reduced CSC in older adults with hearing loss compared to the younger group in our previous study, probably because they had poorer cognitive skills and deployed them differently. Importantly, CSC was not reduced in the older group when listening conditions were optimal. Visual cues improved CSC more for this group than for the younger group in our previous study. CSC of older adults with hearing loss was not generally related to WMC but it was consistently related to episodic long term memory, suggesting that the efficiency of this processing bottleneck is important for executive processing of speech in this group.
Vitamin D levels and risk of multiple sclerosis in patients with clinically isolated syndromes

Background: Growing evidence suggests that vitamin D deficiency may be one of the most important environmental factors for the development of multiple sclerosis (MS). Objectives: The objectives of this paper are to evaluate serum 25-hydroxyvitamin D (25(OH)D) levels in patients with clinically isolated syndromes (CIS) and to examine whether they are related to MS risk. Methods: This is a retrospective study of 100 CIS patients hospitalized from 2000 to 2009 at San Raffaele Hospital, Milan, Italy. We evaluated baseline 25(OH)D level as well as clinical, brain magnetic resonance imaging (MRI) and cerebrospinal fluid (CSF) data. Results: A total of 52% of CIS patients had vitamin D deficiency (25(OH)D < 50 nmol/l). During follow-up (median: 7.17 years), 55 patients developed clinically definite MS (CDMS). Patients with very low (< 10th percentile) and low (< 25th percentile) 25(OH)D levels were particularly at risk of CDMS (HRs (95% CIs): 2.12 (0.91–4.96) and 1.61 (0.85–3.03), respectively), while no further reduction in the HRs of disease was observed at high levels of 25(OH)D. This association was even stronger after adjustment for additional risk factors for CDMS development (HRs (95% CIs) for 25(OH)D levels < 10th and 25th percentiles: 3.34 (1.32–8.45) and 2.04 (0.96–4.36), respectively). Conclusion: Low serum vitamin D is associated with increased MS risk in patients with CIS.
Phagocytosis: receptors, signal integration, and the cytoskeleton

Phagocytosis is a remarkably complex and versatile process: it contributes to innate immunity through the ingestion and elimination of pathogens, while also being central to tissue homeostasis and remodeling by clearing effete cells. The ability of phagocytes to perform such diverse functions rests, in large part, on their vast repertoire of receptors. In this review, we address the various receptor types, their mobility in the plane of the membrane, and two modes of receptor crosstalk: priming and synergy. A major section is devoted to the actin cytoskeleton, which not only governs receptor mobility and clustering but also is instrumental in particle engulfment. Four stages of the actin remodeling process are identified and discussed: (i) the ‘resting’ stage that precedes receptor engagement, (ii) the disruption of the cortical actin prior to formation of the phagocytic cup, (iii) the actin polymerization that propels pseudopod extension, and (iv) the termination of polymerization and removal of preassembled actin that are required for focal delivery of endomembranes and phagosomal sealing. These topics are viewed in the larger context of the differentiation and polarization of the phagocytic cells.