Miracle-dz/UniFAR-FTUs huggingface dataset:
The 5300-year-old Helicobacter pylori genome of the Iceman

Stomach ache for a European mummy Five thousand years ago in the European Alps, a man was shot by an arrow, then clubbed to death. His body was subsequently mummified by ice until glacier retreat exhumed him in 1991. Subsequently, this ancient corpse has provided a trove of intriguing information about copper-age Europeans. Now, Maixner et al. have identified the human pathogen Helicobacter pylori within the mummy's stomach contents. The strain the “Iceman” hosted appears to most closely resemble pathogenic Asian strains found today in Central and Southern Asia. Science, this issue p. 162 Mummified remains from the Alps reveal an unexpected history for a human pathogen. The stomach bacterium Helicobacter pylori is one of the most prevalent human pathogens. It has dispersed globally with its human host, resulting in a distinct phylogeographic pattern that can be used to reconstruct both recent and ancient human migrations. The extant European population of H. pylori is known to be a hybrid between Asian and African bacteria, but there exist different hypotheses about when and where the hybridization took place, reflecting the complex demographic history of Europeans. Here, we present a 5300-year-old H. pylori genome from a European Copper Age glacier mummy. The “Iceman” H. pylori is a nearly pure representative of the bacterial population of Asian origin that existed in Europe before hybridization, suggesting that the African population arrived in Europe within the past few thousand years.
Combined Use of Experimental Pain and Visual Analogue Scales in Providing Standardized Measurement of Clinical Pain

Myofascial pain dysfunction (MPD) patients, pain-free control subjects, and low back patients from a previous study were compared for visual analogue scale (VAS) responses to experimental pain (43–51°C temperatures) and clinical pain. MPD, low back pain, and control groups' nociceptive temperature-VAS response functions were all power functions with exponents of 2.1 for VAS-sensory-intensity responses, and 2.4–2.7 for VAS-affective responses. MPD patients' VAS-sensory responses to clinical pain, direct temperature matches to clinical pain, and temperature-VAS response function were internally consistent. The similar nociceptive stimulus-VAS response functions and consistent use of VAS to rate experimental and clinical pain provide a standardized procedure, whereby intensities of different types of pain can be accurately compared.
A 45nm 1.3GHz 16.7 double-precision GFLOPS/W RISC-V processor with vector accelerators

A 64-bit dual-core RISC-V processor with vector accelerators has been fabricated in a 45nm SOI process. This is the first dual-core processor to implement the open-source RISC-V ISA designed at the University of California, Berkeley. In a standard 40nm process, the RISC-V scalar core scores 10% higher in DMIPS/MHz than the Cortex-A5, ARM's comparable single-issue in-order scalar core, and is 49% more area-efficient. To demonstrate the extensibility of the RISC-V ISA, we integrate a custom vector accelerator alongside each single-issue in-order scalar core. The vector accelerator is 1.8× more energy-efficient than the IBM Blue Gene/Q processor, and 2.6× more than the IBM Cell processor, both fabricated in the same process. The dual-core RISC-V processor achieves maximum clock frequency of 1.3GHz at 1.2V and peak energy efficiency of 16.7 double-precision GFLOPS/W at 0.65V with an area of 3mm2.
Antibiotic Management of Methicillin-Resistant Staphylococcus aureus–Associated Acute Pulmonary Exacerbations in Cystic Fibrosis

Objective: To review the treatment of methicillin-resistant Staphylococcus aureus (MRSA)–associated acute pulmonary exacerbations (APEs) in cystic fibrosis (CF). Data Sources: A search of PubMed, MEDLINE, Cochrane Library and Clinicaltrials.gov databases through November 2014 was conducted using the search terms Staphylococcus aureus, methicillin-resistant Staphylococcus aureus, pulmonary exacerbations, and cystic fibrosis. Study Selection and Data Extraction: All English-language research articles, case reports, and case series were evaluated. A total of 185 articles were identified related to MRSA and CF; 30 articles that studied treatments of MRSA APE in CF were included. Data Synthesis: The persistent presence of MRSA in the respiratory tract of patients with CF has been associated with higher morbidity and an increased risk of death. Limited clinical data exist supporting the efficacy of any specific antimicrobial currently available for the treatment of APE secondary to MRSA. Conclusions: Data extrapolated from other populations suggest that vancomycin and linezolid are appropriate first-line treatment options for the treatment of APE secondary to MRSA. Second-line options include doxycycline or minocycline and trimethoprim/sulfamethoxazole, each of which may be useful in patients coinfected with other respiratory pathogens, for which they may provide overlapping coverage. Ceftaroline and ceftobiprole are newer antibiotics that appear to have a potential role in the treatment of APE in CF, but the latter is not currently available to the US market. Although potentially useful, clindamycin is limited by high rates of resistance, telavancin is limited by its toxicity profile, and tigecycline is limited by a lack of demonstrated efficacy for infections that are similar to that seen in the CF population. Studies investigating the clinical utility of the above-cited antibiotics for APE in CF secondary to MRSA are desperately needed to broaden the treatment armamentarium for this medical condition.
Self-organization of river channels as a critical filter on climate signals

Filtering out the effect of large floods Large floods should seemingly influence the depth and width of rivers. Phillips and Jerolmack, however, suggest that the self-organization of bedrock river channels blunts the impact of extreme rainfall events. River channel geometries from a wide range of course-grained rivers across the United States show that larger floods have very limited additional impact on channel geometry. River channel sculpting does increase as flood size increases, but the effect is most pronounced for moderate floods. This relationship may explain the long-term stability of rivers across shifts in climate. Science, this issue p. 694 A wide-ranging assessment of rivers in the United States suggests that erosion and climate become decoupled during large rainfall events. Spatial and temporal variations in rainfall are hypothesized to influence landscape evolution through erosion and sediment transport by rivers. However, determining the relation between rainfall and river dynamics requires a greater understanding of the feedbacks between flooding and a river’s capacity to transport sediment. We analyzed channel geometry and stream-flow records from 186 coarse-grained rivers across the United States. We found that channels adjust their shape so that floods slightly exceed the critical shear velocity needed to transport bed sediment, independently of climatic, tectonic, and bedrock controls. The distribution of fluid shear velocity associated with floods is universal, indicating that self-organization of near-critical channels filters the climate signal evident in discharge. This effect blunts the impact of extreme rainfall events on landscape evolution.
Ciclofotocoagulacao com laser diodo em glaucoma refratario, resultado a longo prazo

PURPOSE: To report long-term experience with cyclophotocoagulation using diode laser in refractory glaucomas. METHODS: We selected cases of refractory glaucoma with indication for cyclophotocoagulation (CPC) with diode laser using a G probe (Iris Medical). All procedures were performed by the same surgeon: twenty applications of 2000 mW power at 270- degree extension. The probe placed set at 1.5 mm from the limbus during 2.0 a 2.5 s. Only cases with at least 6 months of follow-up were included. The procedure was considered successful when IOP was < 24 mmHg or decrease was larger or equal to 30% of the initial IOP with remission of symptoms. Only 25 patients (18.75%) concluded the study (36 months). RESULTS: One hundred and thirty cases had a mean follow-up of 18,1 ± 9,6 months with 116 (87.2%) successful cases and 17 (12,7%) insuccess ful cases. Initial and final IOP were, 48.20 ± 12.11mmHg and 19.93 ± 11,93mmHg respectively (p < 0.0001). Main complications were: "Phthisis bulbi" in 7 (5.2%) cases and long-term hypotony in 6 (4.5%) cases. CONCLUSIONS: Considering the severity of our cases, we conclude that the long-term results of cyclophotocoagulation with diode laser for refractory glaucomas were satisfactory, with an acceptable incidence of complications.
Sequential ionic and conformational signaling by calcium channels drives neuronal gene expression

Calcium channels deliver a one-two punch To help generate long-lasting neuronal plasticity, CaV1.2 (L-type) calcium channels link electrical activity to nuclear gene expression. However, exactly how this coupling works is not fully understood. Li et al. developed a strategy to control two voltage-dependent signals—Ca2+ influx and non-ionic conformational changes—separately. The combinatorial delivery of both signals was required to maximize transcription. Ca2+ influx first mobilized the kinase CaMKII from the cytosol. This allowed subsequent voltage-dependent conformational changes to localize the kinase at CaV1.2 signaling hot spots. Abnormality of nonionic conformational signaling is associated with neurological dysfunction in Timothy syndrome, a highly penetrant form of autism-spectrum disorder. Science, this issue p. 863 CaV1.2 channels rely on both conformational signaling and Ca2+ flux to mediate neuronal plasticity. Voltage-gated CaV1.2 channels (L-type calcium channel α1C subunits) are critical mediators of transcription-dependent neural plasticity. Whether these channels signal via the influx of calcium ion (Ca2+), voltage-dependent conformational change (VΔC), or a combination of the two has thus far been equivocal. We fused CaV1.2 to a ligand-gated Ca2+-permeable channel, enabling independent control of localized Ca2+ and VΔC signals. This revealed an unexpected dual requirement: Ca2+ must first mobilize actin-bound Ca2+/calmodulin-dependent protein kinase II, freeing it for subsequent VΔC-mediated accumulation. Neither signal alone sufficed to activate transcription. Signal order was crucial: Efficiency peaked when Ca2+ preceded VΔC by 10 to 20 seconds. CaV1.2 VΔC synergistically augmented signaling by N-methyl-d-aspartate receptors. Furthermore, VΔC mistuning correlated with autistic symptoms in Timothy syndrome. Thus, nonionic VΔC signaling is vital to the function of CaV1.2 in synaptic and neuropsychiatric processes.
Sustaining Female Helicopter Pilot Performance With Dexedrine During Sleep Deprivation

To investigate the efficacy of Dexedrine for maintaining the performance of sleep deprived female aviators, 6 female UH-60 pilots were exposed to 2 40-hr sleep deprivation periods during which they alternately received Dexedrine (3 10mg doses) or placebo. Dexedrine improved 6 of 9 flight simulator maneuvers and enhanced general levels of alertness as measured by EEG and Profile of Mood States assessments. The results from a cognitive test were negligible and inconsistent, probably because of the short test duration. Overall, it appeared that Dexedrine effectively sustained the performance, alertness, and mood of female UH-60 pilots despite short-term sleep loss. There were no problematic side effects.
Reconfigurable 96×128 active pixel sensor with 2.1µW/mm2 power generation and regulated multi-domain power delivery for self-powered imaging

We present an energy harvesting system comprising a dual purpose CMOS active pixel sensor (APS) array, and a combined energy extractor and multi domain voltage regulator on a single die in 130nm technology. The reconfigurable image sensor is a 128 × 96 pixel array. The array captures image and is reconfigured to form an on-chip photovoltaic cell to harvest energy. It generates 2. 1μW peak power at 300mV with 200klux illuminance. The generated voltage is used as the input of the switching energy extractor that boosts the voltage up to 3.3V and stores the energy in the storage element (battery/super capacitor). The stored energy is then supplied to the load at three independent domains using the single inductor multi-output (SIMO) buck regulator. Both the SIMO buck and the energy-harvesting boost use the only inductor in the system through internally managed time-multiplexing mechanism. This prototype demonstrates a solution for low frame rate, energy autonomous imaging applications including distributed wireless sensor node and IoT electronics.
A peptide encoded by a transcript annotated as long noncoding RNA enhances SERCA activity in muscle

Another micropeptide flexes its muscle Genome annotation is a complex but imperfect art. Attesting to its limitations is the growing evidence that certain transcripts annotated as long noncoding RNAs (lncRNAs) in fact code for small peptides with biologically important functions. One such lncRNA-derived micropeptide in mammals is myoregulin, which reduces muscle performance by inhibiting the activity of a key calcium pump. Nelson et al. describe the opposite activity in a second lncRNA-derived micropeptide in mammalian muscle, called DWORF (see the Perspective by Payre and Desplan). This peptide enhances muscle performance by activating the same calcium pump. DWORF may prove to be useful in improving the cardiac muscle function of mammals with heart disease. Science, this issue p. 271; see also p. 226 A long noncoding RNA encodes a small peptide that activates a calcium pump regulating muscle contraction. [Also see Perspective by Payre and Desplan] Muscle contraction depends on release of Ca2+ from the sarcoplasmic reticulum (SR) and reuptake by the Ca2+adenosine triphosphatase SERCA. We discovered a putative muscle-specific long noncoding RNA that encodes a peptide of 34 amino acids and that we named dwarf open reading frame (DWORF). DWORF localizes to the SR membrane, where it enhances SERCA activity by displacing the SERCA inhibitors, phospholamban, sarcolipin, and myoregulin. In mice, overexpression of DWORF in cardiomyocytes increases peak Ca2+ transient amplitude and SR Ca2+ load while reducing the time constant of cytosolic Ca2+ decay during each cycle of contraction-relaxation. Conversely, slow skeletal muscle lacking DWORF exhibits delayed Ca2+ clearance and relaxation and reduced SERCA activity. DWORF is the only endogenous peptide known to activate the SERCA pump by physical interaction and provides a means for enhancing muscle contractility.
Evaluation of Primary Screening Test for Platelet Homeostasis in Patients with Chronic Kidney Disease

This observational study was done on 50 cases of predialytic chronic kidney disease (CKD) patients. The aim of the study was to determination of total platelet count and bleeding time, comparison of the platelet count and bleeding time with the severity of chronic kidney disease. The mean age of the patients was 41.22±2.0 years, mean haemoglobin 4.96 ±0.32gm/dl, serum creatinine430.74± 11.92 μmol/L, platelet count 246.50 ± 13.63x10 9 /L and bleeding time were 4.13± 0.28 min respectively. Thrombocytopenia ( 9min) 6(12%) cases , among them only 4(8% ) cases were thrombocytopenic. There was no significant relationship between platelet count and serum creatinine. No correlation was found between platelet count and bleeding time. No significant correlation was also found in Bleeding time and creatinine. Therefore, it can be concluded that platelet count is highly variable in chronic kidney disease and it is not a reliable screening test for bleeding diathesis in chronic kidney disease patients. Bleeding time is the best platelet function test that correlates clinical bleeding. DOI: http://dx.doi. org/10.3329/bjmed.v21i2. 13610 Bangladesh J Medicine 2010; 21: 55-57
Identifying and Measuring Multilevel Influences on College-Aged Athletes’ Multiple Health Behavior: A Pilot Study

The current study gathered preliminary data relative to the influences on intercollegiate athletes’ multiple health behavior. A secondary objective was to inform future measurement of identified factors. A sample of 20 intercollegiate athletes participated in an open-ended survey, followed by a corresponding focus groups (≈90-minute). Qualitative data were gathered relative to the factors impacting athletes’ excessive alcohol intake, fruit and vegetable consumption (FVC), and maintenance of physical activity after college. In general, participating athletes reported influences within their social and physical environments (friends, bar accessibility, etc.) as the leading enablers of their excessive alcohol intake, while individual level influences were the most salient reasons not to drink excessively (responsibilities, health, etc.). Individual characteristics (taste preference, health, and expense) and the physical environment (availability and accessibility) were reported as the most salient levels of influence on athletes’ FVC. And when anticipating future maintenance of physical activity, athletes mostly reported individual level influences (outcome expectation, intrinsic motivation, etc.), with mention of family and friend influences. An in-depth comparison of current outcomes to similar research among young adult and athlete populations is provided, including validated measurement scales and future research suggestions. Current results provide an essential foundation for progressive research examinations among similar populations.
Impact of a Vitamin D Protocol in Pregnancy at an Urban Women’s Health Clinic

Background: Adequate vitamin D levels are important during pregnancy for maternal and fetal health. The prevalence of vitamin D deficiency and appropriate treatment during pregnancy are not well documented. Objectives: This study aims to identify the prevalence of vitamin D deficiency in pregnant women and analyze the impact of a vitamin D protocol on achieving sufficient vitamin D levels. Methods: A retrospective chart review was conducted among 200 women who received prenatal care between April 1, 2011, and December 1, 2012 (preprotocol) and July 1, 2013, and June 30, 2014 (postprotocol). In each sample period, 100 women were included. Women were included if they had 2 vitamin D levels drawn during pregnancy. Maternal age, ethnicity, vitamin D levels, gestational age at each level, and the status of vitamin D supplement were controlled for. Results: Women in the preprotocol group achieving sufficiency (25[OH]D ≥ 30 ng/mL) increased from 43% to 60%. In the postprotocol group, sufficiency increased from 19% to 69%. Adherence to the protocol dose was highest in women who were initially deficient (25[OH]D ≤ 20 ng/mL), and correlation between adherence to the protocol dose and achievement of sufficiency was also highest in the group of women who were initially deficient. Conclusions: Vitamin D deficiency was prevalent (25% total) in this population. Implementation of a clinic-wide protocol for vitamin D supplementation during pregnancy resulted in a nonsignificant increase in the percentage of women achieving vitamin D sufficiency.
Resource Allocation for Joint Transmitter and Receiver Energy Efficiency Maximization in Downlink OFDMA Systems

This paper investigates the joint transmitter and receiver optimization for the energy efficiency (EE) in orthogonal frequency-division multiple-access (OFDMA) systems. We first establish a holistic power dissipation model for OFDMA systems, including the transmission power, signal processing power, and circuit power from both the transmitter and receiver sides, while existing works only consider the one side power consumption and also fail to capture the impact of subcarriers and users on the system EE. The EE maximization problem is formulated as a combinatorial fractional problem that is NP-hard. To make it tractable, we transform the problem of fractional form into a subtractive-form one by using the Dinkelbach transformation and then propose a joint optimization method, which leads to the asymptotically optimal solution. To reduce the computational complexity, we decompose the joint optimization into two consecutive steps, where the key idea lies in exploring the inherent fractional structure of the introduced individual EE and the system EE. In addition, we provide a sufficient condition under which our proposed two-step method is optimal. Numerical results demonstrate the effectiveness of proposed methods, and the effect of imperfect channel state information is also characterized.
Artificial Noise: Transmission Optimization in Multi-Input Single-Output Wiretap Channels

We analyze and optimize the secrecy performance of artificial noise (AN) in multi-input single-output wiretap channels with multiple antennas at the transmitter and a single antenna at the receiver and the eavesdropper. We consider two transmission schemes: 1) an on-off transmission scheme with a constant secrecy rate for all transmission periods, and 2) an adaptive transmission scheme with a varying secrecy rate during each transmission period. For the on-off transmission scheme, an easy-to-compute expression is derived for the hybrid outage probability, which allows us to evaluate the transmission outage probability and the secrecy outage probability. For the adaptive transmission scheme where transmission outage does not occur, we derive a closed-form expression for the secrecy outage probability. Using these expressions, we determine the optimal power allocation between the information signal and the AN signal and also determine the optimal secrecy rate such that the effective secrecy throughput is maximized for both transmission schemes. We show that the maximum effective secrecy throughput requires more power to be allocated to the AN signal when the quality of the transmitter-receiver channel or the transmitter-eavesdropper channel improves. We also show that both transmission schemes achieve a higher maximum effective secrecy throughput while incurring a lower secrecy outage probability than existing schemes.
Airway acidification initiates host defense abnormalities in cystic fibrosis mice

Airway infections put to an acid test Most people with cystic fibrosis suffer from chronic respiratory infections. The mechanistic link between this symptom and the genetic cause of the disease (mutations that compromise the function of the cystic fibrosis transmembrane conductance regulator, CFTR) is not fully understood. Studying animal models, Shah et al. find that in the absence of functional CFTR, the surface liquid in the airways becomes acidic, which impairs host defenses against infection. This acidification occurs through the action of a proton pump called ATP12A. Molecules inhibiting ATP12A could potentially be developed into useful drugs. Science, this issue p. 503 A specific proton pump that acidifies airway surface liquids promotes respiratory infections in cystic fibrosis. Cystic fibrosis (CF) is caused by mutations in the gene that encodes the cystic fibrosis transmembrane conductance regulator (CFTR) anion channel. In humans and pigs, the loss of CFTR impairs respiratory host defenses, causing airway infection. But CF mice are spared. We found that in all three species, CFTR secreted bicarbonate into airway surface liquid. In humans and pigs lacking CFTR, unchecked H+ secretion by the nongastric H+/K+ adenosine triphosphatase (ATP12A) acidified airway surface liquid, which impaired airway host defenses. In contrast, mouse airways expressed little ATP12A and secreted minimal H+; consequently, airway surface liquid in CF and non-CF mice had similar pH. Inhibiting ATP12A reversed host defense abnormalities in human and pig airways. Conversely, expressing ATP12A in CF mouse airways acidified airway surface liquid, impaired defenses, and increased airway bacteria. These findings help explain why CF mice are protected from infection and nominate ATP12A as a potential therapeutic target for CF.