Miracle-dz/UniFAR-FTUs huggingface dataset:
Photocross-links between Single-stranded DNA and Escherichia coli RecA Protein Map to Loops L1 (Amino Acid Residues 157-164) and L2 (Amino Acid Residues 195-209) (*)

To function as a repair and recombination protein, RecA has to be assembled as an active filament on single-stranded DNA in the presence of ATP or its analogs. We have identified amino acids in the primary DNA binding site of RecA that interact with single-stranded DNA by photocross-linking. A nucleoprotein complex consisting of RecA protein bound to a monosubstituted oligonucleotide bearing a 5-iododeoxyuracil cross-linking moiety was irradiated with long wavelength ultraviolet radiation to effect cross-linking with RecA protein. Subsequent trypsin digestion, followed by purification and peptide sequencing, revealed the cross-linking of two independent peptides, amino acid residues 153-169 and 199-216. Met164 from loop L1 and Phe203 from loop L2 were determined to be the exact points of cross-linking. Thus, our data confirm and extend predictions about the DNA binding domain of RecA protein based on the molecular structure of RecA (Story, R. M., Weber, I. T., and Steitz, T. A.(1992) Nature 355, 318-325). [Medline]
Development of Multiplexed Marker Sets to Identify the Most Relevant Poplar Species for Breeding

Within the genus Populus, about 30 species are classified into six sections, of which some are cross-compatible. Besides naturally occurring hybrids, huge breeding programs have led to a high number of artificially produced hybrids, for which the determination of genetically involved species by morphological characteristics is often difficult. This necessitates the use of molecular markers for the identification of both maternal as well as paternal species, and in the case of complex hybrids, the genealogy. For this reason, we developed new chloroplast and nuclear markers for the differentiation of up to 19 poplar species, with one to 32 individuals per species regularly used in breeding programs based on already known barcoding, other chloroplast regions, and nuclear genes of interest. We developed methods to identify species by either species-specific nucleotide variations or, when no initial information for the species was given, by using a set of markers either in a procedure of exclusion or in a multiplexed marker set. The developed markers can all be used with low-cost equipment, and some can additionally be applied using a genetic analyzer. We combined these markers in multiplexes for a very fast and easy-to-use application for the identification of poplar species and their hybrids.
The Nature of Fatigue in Chronic Fatigue Syndrome

In this article, we report the findings of our study on the nature of fatigue in patients diagnosed with chronic fatigue syndrome. Using ethnoscience as a design, we conducted a series of unstructured interviews and card sorts to learn more about how people with chronic fatigue syndrome describe fatigue. Participants (N = 14) described three distinct domains: tiredness, fatigue, and exhaustion. Most participants experienced tiredness prior to diagnosis, fatigue during daily life, and exhaustion after overexertion. We also discuss participants’ ability to adapt to a variety of stressors and prevent shifts to exhaustion, and relate our findings to stress theory and other current research. Primary strategies that promoted adaptation to stressors included pacing and extended rest periods. These findings can aid health care professionals in detecting impending shifts between tiredness, fatigue, and exhaustion and in improving adaptive strategies, thereby improving quality of life.
Konversi Lahan Pertanian Dan Perubahan Struktur Agraria (Studi Kasus di Kelurahan Mulyaharaja, Kecamatan Bogor Selatan, Kota Bogor, Jawa Barat)

Tulisan ini merupakan hasil penelitian yang bertujuanmenganalisis konversi lahan pertanian dan perubahan struktur agraria di Kelurahan Mulyaharja. Strategi penelitian yang digunakan adalah pendekatan kualitati.Dampak konversi lahan pertanian di Kelurahan Muliahardja adalah ketimpangan struktur agraria lahan terhadap kehidupan masyarakat menyangkut perubahan pola penguasaan lahan, pola nafkah dan hubungan pola produksi. Ketimpangan struktur agraria berimplikasi terhadap kehidupan/kesejahteraan masyarakat. Tesis yang ‘dibangun’ adalah ‘keadilan agraria’. Inti/gagasan tesis ini adalah perubahan struktur agraria yang menyebabkan tekanan sosial yang tidak merata, dimana kaum berpendapatan rendah/miskin adalah penderita utama atas hadirnya perubahan tersebut (fakta-fakta ketidak-adilan agraria) Harapan ke depan adalah proses pembangunan yang memperhatikan ‘keadilan agraria’ (pembangunan agraria yang memihak pada kaum miskin.
Critical Issues For Understanding Particle Acceleration in Impulsive Solar Flares

This paper, a review of the present status of existing models for particle acceleration during impulsive solar flares, was inspired by a week-long workshop held in the Fall of 1993 at NASA Goddard Space Flight Center. Recent observations from Yohkoh and the Compton Gamma Ray Observatory, and a reanalysis of older observations from the Solar Maximum Mission, have led to important new results concerning the location, timing, and efficiency of particle acceleration in flares. These are summarized in the first part of the review. Particle acceleration processes are then discussed, with particular emphasis on new developments in stochastic acceleration by magnetohydrodynamic waves and direct electric field acceleration by both sub- and super-Dreicer electric fields. Finally, issues that arise when these mechanisms are incorporated into the large-scale flare structure are considered. Stochastic and super-Dreicer acceleration may occur either in a single large coronal reconnection site or at multiple “fragmented” energy release sites. Sub-Dreicer acceleration requires a highly filamented coronal current pattern. A particular issue that needs to be confronted by all theories is the apparent need for large magnetic field strengths in the flare energy release region.
Use of intrathecal SNX-111, a novel, N-type, voltage-sensitive, calcium channel blocker, in the management of intractable brachial plexus avulsion pain.

OBJECTIVE The objective was to assess the analgesic, antihyperesthesic, and anti-allodynic properties of SNX-111 in neuropathic pain. DESIGN We describe a patient with refractory, severe deafferentation pain successfully treated with SNX-111 in an open-label, baseline-controlled Phase I/II trial. SETTING The patient was hospitalized for treatment and observation. PATIENT The patient was a 43-year-old man with intractable deafferentation pain of 23 years' duration secondary to brachial plexus avulsion. INTERVENTION SNX-111, the first neuron-specific, N-type, voltage-sensitive calcium channel blocker developed for clinical use, was administered by continuous, constant-rate, intrathecal infusion via an indwelling cervical catheter. OUTCOME MEASURES The primary outcome measures were the Visual Analog Scales of Pain Intensity (VASPI) and Pain Relief (VASPR). RESULTS The patient experienced complete pain relief (VASPI = 0.0 cm and VASPR = 10.0 cm) with elimination of hyperesthesia and allodynia. CONCLUSIONS SNX-111, administered intrathecally by continuous, constant-rate infusion, produced dose-dependent pain relief in a 43-year-old male patient with a 23-year history of intractable deafferentation and phantom limb pain secondary to brachial plexus avulsion and subsequent amputation. Dizziness, blurred vision, and lateral-gaze nystagmus were dose-dependent side effects that resolved with decreasing dose levels. Complete pain relief was achieved in this patient without side effects after dose adjustment. We conclude that SNX-111 is a potent analgesic, antihyperesthesic, and antiallodynic agent. Controlled studies of SNX-111 in patients with malignant and nonmalignant pain syndromes are warranted and are under way.
Maternal alcohol drinking pattern during pregnancy and the risk for an offspring with an isolated congenital heart defect and in particular a ventricular septal defect or an atrial septal defect.

BACKGROUND This cohort study examines the possible association between maternal alcohol intake, including binge drinking, during pregnancy, and the subsequent risk of having a child with an isolated congenital heart defect and, more specifically, with the isolated form of ventricular septal defect (VSD) or of an atrial septal defect (ASD). METHODS Participants were 80,346 pregnant women who were enrolled into the Danish National Birth Cohort in 1996-2002 and gave birth to a live-born singleton without any chromosome anomalies. Twice during pregnancy these women were asked about their intake of alcohol. Few (if any) women with an excessive/abusive intake of alcohol were enrolled into the Danish National Birth Cohort. RESULTS Through linkage with the National Hospital Discharge Registry, we identified 477 infants with a diagnosis of isolated congenital heart defect registered at any time during their first 3½-years of life; they included 198 infants with a VSD and 145 with an ASD. Neither the number of episodes of binge drinking nor binge drinking during three different developmental periods was associated with VSD or ASD. Women drinking ½-1½, 2, and 3+ drinks of alcohol per week had adjusted prevalence ratios of delivering an infant with a VSD of 1.22 (95% CI = 0.90-1.66); 1.38 (95% CI = 0.83-2.28); and 1.10 (95% CI = 0.54-2.23), respectively. The test for trend was 0.29. CONCLUSIONS Prenatal exposure to low-to-moderate levels of alcohol on a weekly basis or occasional binge drinking during the early part of pregnancy was not statistical significantly associated with the prevalence of isolated VSD and ASD in offspring.
Formulation of a drinkable peanut-based therapeutic food for malnourished children using plant sources

High ingredient costs continue to hamper local production of therapeutic foods (TFs). Development of formulations without milk, the most expensive ingredient, is one way of reducing cost. This study formulated a ready-to-drink peanut-based TF that matched the nutrient composition of F100 using plant sources. Three least cost formulations namely, A, B and C were designed using computer formulation software with peanuts, beans, sesame, cowpeas and grain amaranth as ingredients. A 100 g portion of the TF provided 101–111 kcal, 5 g protein and 5.3–6.5 g fat. Consumer acceptability hedonic tests showed that the products were liked (extremely and moderately) by 62–65% of mothers. These results suggest that nutrient dense TFs formulated from only plant sources have the potential to be used in the rehabilitation phase of the management of malnourished children after clinical testing.
Adaptive Hybrid Methods for Choice-Based Conjoint Analysis: A Comparative Study

Adaptive choice-based conjoint analysis (ACBC) and hybrid individualized two-level choice-based conjoint analysis (HIT-CBC) were developed to improve standard choice-based conjoint analysis through additional interviewing techniques. Both methods have demonstrated their applicability in comparison to standard choice-based conjoint methods. The objective of our study was a direct comparison of the two adaptive hybrid methods ACBC and HIT-CBC. Therefore, we analysed the previous comparative literature on the methods and used the results to conduct both a Monte Carlo simulation study and an empirical study for validity comparisons. The simulation study confirms the vulnerability of HIT-CBC to produce incorrect ratings of respondents in the last part of the questionnaire. The empirical findings reveal an advantage of ACBC in comparison to the current version of HIT-CBC. We conclude that the rating tasks in the last section of HIT-CBC questionnaires reduce the predictive validity of the method and suggest an improvement to HIT-CBC.
Mechanical Circulatory Support Devices

Heart failure (HF) is a global public health concern that has the potential to reach epidemic proportions. The gold standard for treating end-stage HF remains heart transplanta‐ tion. Unfortunately, given the scarcity of available organs, alternative means for providing cardiac support are required. Mechanical circulatory support devices (MCSDs) have the potential to treat many patients with end-stage HF. They replace some of the mechani‐ cal functions of the failing heart to improve cardiac output and organ perfusion. These include the intra-aortic balloon pump, extracorporeal membrane oxygenation, ventric‐ ular assist devices, and the total artificial heart. In this chapter, we will discuss a brief history of MCSD, available devices, indications, patient selection, surgical procedures, postoperative management, complications, and outcomes.
Neurotransmitter Levels and Synaptic Strength at the Drosophila Larval Neuromuscular Junction are not Altered by Mutation in the Sluggish-a Gene, Which Encodes Proline Oxidase and Affects Adult Locomotion

The sluggish-A (slgA) gene of Drosophila melanogaster has been shown to encode for the enzyme proline oxidase, a mitochondrial enzyme which catalyzes the first step in the conversion of L-proline to L-glutamate. The slgA transcript is expressed in both larval and adult Drosophila melanogaster. Mutations in this gene lead to reduced proline oxidase activity and an elevation of free proline levels. Adult mutant flies show a striking reduction of motor activity. Since proline oxidase may contribute to the supply of the neurotransmitter glutamate in the nervous system, a reduction in proline oxidase activity could reduce neural glutamate pools and affect synaptic transmission in neurons utilizing glutamate as a transmitter, including peripheral motor neurons. We tested the hypothesis that glutamate, and synaptic transmission mediated by glutamate, are reduced at synapses of glutamatergic motor neurons in slgA mutants. Levels of glutamate and proline in different cell compartments, and functional properties of synaptic transmission were compared in slgA and control specimens. Proline is elevated in muscle cells of slgA mutants, indicating that the slgA gene regulates tissue proline levels. In nerve terminal varicosities, proline levels were low in both mutants and controls. Glutamate levels in nerve terminal varicosities of slgA mutants and controls were similar. In addition, we found that glutamatergic synaptic transmission at individual nerve endings and at the whole-cell level was similar in slgA mutants and controls. Thus, proline oxidase does not play a major role in generating neuronal glutamate pools at the Drosophila larval neuromuscular junction, and larval neuromuscular performance is not altered significantly in slgA mutants. Metabolic pathways other than that involving proline oxidase are able to sustain glutamatergic synaptic function in Drosophila larvae.
Haploinsufficiency of the LIM domain containing preferred translocation partner in lipoma (LPP) gene in patients with tetralogy of Fallot and VACTERL association

Haploinsufficiency of the LIM Domain Containing Preferred Translocation Partner in Lipoma (LPP) Gene in Patients With Tetralogy of Fallot and VACTERL Association Cammon B. Arrington, Ankita Patel, Carlos A. Bacino, and Neil E. Bowles* Division of Cardiology, Department of Pediatrics, University of Utah School of Medicine, Salt Lake City, Utah Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
Functional recordings from awake, behaving rodents through a microchannel based regenerative neural interface

Objective. Neural interface technologies could provide controlling connections between the nervous system and external technologies, such as limb prosthetics. The recording of efferent, motor potentials is a critical requirement for a peripheral neural interface, as these signals represent the user-generated neural output intended to drive external devices. Our objective was to evaluate structural and functional neural regeneration through a microchannel neural interface and to characterize potentials recorded from electrodes placed within the microchannels in awake and behaving animals. Approach. Female rats were implanted with muscle EMG electrodes and, following unilateral sciatic nerve transection, the cut nerve was repaired either across a microchannel neural interface or with end-to-end surgical repair. During a 13 week recovery period, direct muscle responses to nerve stimulation proximal to the transection were monitored weekly. In two rats repaired with the neural interface, four wire electrodes were embedded in the microchannels and recordings were obtained within microchannels during proximal stimulation experiments and treadmill locomotion. Main results. In these proof-of-principle experiments, we found that axons from cut nerves were capable of functional reinnervation of distal muscle targets, whether regenerating through a microchannel device or after direct end-to-end repair. Discrete stimulation-evoked and volitional potentials were recorded within interface microchannels in a small group of awake and behaving animals and their firing patterns correlated directly with intramuscular recordings during locomotion. Of 38 potentials extracted, 19 were identified as motor axons reinnervating tibialis anterior or soleus muscles using spike triggered averaging. Significance. These results are evidence for motor axon regeneration through microchannels and are the first report of in vivo recordings from regenerated motor axons within microchannels in a small group of awake and behaving animals. These unique findings provide preliminary evidence that efferent, volitional motor potentials can be recorded from the microchannel-based peripheral neural interface; a critical requirement for any neural interface intended to facilitate direct neural control of external technologies.
The Criterion Validity, Reliability, and Feasibility of an Instrument for Assessing the Nursing Intensity in Perioperative Settings

Patient classification systems generate information for staff allocation based on a patient's care needs. This study aims to test further the instrument for assessing nursing intensity (NI) in perioperative settings. Nine operating departments from five university hospitals were involved. The perioperative nurses gathered data from patients (N = 876) representing different fields of surgery. Reliability was tested by parallel classifications (n = 144). Also, the users' (n = 40) opinions were surveyed. The results support the predictive validity and interrater reliability of the instrument. The nurses considered the instrument feasible to use. The patients' low ASA class did not automatically signify low NI; however, high ASA class was more frequently associated with high intraoperative NI. Intraoperative NI indicated the length of the postanaesthesia care and the type of the follow-up unit. Parallel classifications ensured the homogenous use of the instrument. The use of the instrument is recommended.
Crestal bone loss evaluation in osseotite expanded platform implants: a 5-year study.

OBJECTIVE The aim of this prospective clinical study was to evaluate the survival rates at 5 years of expanded platform implants placed in the anterior zone of the maxilla and immediately restored with single crowns. MATERIALS AND METHODS Implants incorporating the platform-switching concept were placed in fresh extraction sockets in the maxillary arch, with each patient receiving a provisional restoration immediately after implant placement. After 15 days, final screwed restorations were inserted. Mesial and distal bone heights were evaluated using digital radiography on the day following implant placement and at 1, 3, 6, 9, 12, 24, 36 months and 5 years. Primary stability was measured with resonance frequency analysis (RFA) using the Osstell Mentor device. Sixty-four implants were placed in 32 men and 32 women ranging in age between 29 and 60 (mean: 39.64 ± 5.16 years). RESULTS Mean mesial bone loss was 0.08 mm (SD 0.42). Mean distal bone loss was 0.14 mm (SD 0.56). Over the course of the 5 years, the mean RFA value was 72.5 ± 3.1 SD. CONCLUSION The platform-switched implants remained stable over the course of 5 years and had an overall survival rate of 97.1%.
Genetic mapping of polyphenol oxidase in tetraploid wheat.

Pasta colour is one of the main factors influencing pasta quality. It is the product of a desirable yellow component, an undesirable brown component and, under some drying conditions, a red component. The brown colour depends on enzymatic and chemical factors. Polyphenol oxidase (PPO; E.C. 1.14.18.1) is one of the enzymatic factors. It is mainly localised in the peripheral part of the wheat kernel, and is involved in the oxidation of endogenous wheat phenolic compounds resulting in the production of highly coloured products. Therefore, a knowledge of the genetic control of PPO activity could enable the developing of better strategies in breeding programs to reduce pasta darkening. The aim of this study was to map the gene(s) affecting PPO activity using a set of recombinant inbred (RI) lines, derived from a cross between Triticum turgidum L. var. durum cultivar Messapia and the accession MG4343 of Triticum turgidum L. var. dicoccoides. After performing linkage analysis, the gene for high PPO activity was mapped on the long arm of the chromosome 2A and its characteristic was found highly associated to the RFLP marker Xutv1427-2A, with a value of LOD equal to 29.84. The identification of molecular markers linked to loci controlling the PPO activity may potentially accelerate wheat breeding since the selection of plants can be carried out by genotype rather than phenotype.
No Dose-Response Effect of Carbohydrate Mouth Rinse Concentration on 5-km Running Performance in Recreational Athletes

Abstract Clarke, ND, Thomas, JR, Kagka, M, Ramsbottom, R, and Delextrat, A. No dose-response effect of carbohydrate mouth rinse concentration on 5-km running performance in recreational athletes. J Strength Cond Res 31(3): 715–720, 2017—Oral carbohydrate rinsing has been demonstrated to provide beneficial effects on exercise performance of durations of up to 1 hour, albeit predominately in a laboratory setting. The aim of the present study was to investigate the effects of different concentrations of carbohydrate solution mouth rinse on 5-km running performance. Fifteen healthy men (n = 9; mean ± SD age; 42 ± 10 years; height, 177.6 ± 6.1 cm; body mass, 73.9 ± 8.9 kg) and women (n = 6; mean ± SD age, 43 ± 9 years; height, 166.5 ± 4.1 cm; body mass, 65.7 ± 6.8 kg) performed a 5-km running time trial on a track on 4 separate occasions. Immediately before starting the time trial and then after each 1 km, subjects rinsed 25 ml of 0, 3, 6, or 12% maltodextrin for 10 seconds. Mouth rinsing with 0, 3, 6, or 12% maltodextrin did not have a significant effect on the time to complete the time trial (0%, 26:34 ± 4:07 minutes:seconds; 3%, 27:17 ± 4:33 minutes:seconds; 6%, 27:05 ± 3:52 minutes:seconds; 12%, 26:47 ± 4.31 minutes:seconds; p = 0.071; = 0.15), heart rate (p = 0.095; = 0.16), rating of perceived exertion (p = 0.195; = 0.11), blood glucose (p = 0.920; = 0.01), and blood lactate concentration (p = 0.831; = 0.02), with only nonsignificant trivial to small differences between concentrations. Results of this study suggest that carbohydrate mouth rinsing provides no ergogenic advantage over an acaloric placebo (0%) and that there is no dose-response relationship between carbohydrate solution concentration and 5-km track running performance.