Miracle-dz/UniFAR-FTUs huggingface dataset:
Deep-Sea Temperature and Ice Volume Changes Across the Pliocene-Pleistocene Climate Transitions

Stepping Down Earth's environment changed markedly over the past 5.2 million years, when a permanent ice sheet has developed in the Northern Hemisphere and the glacial cycle has changed its period from roughly every 40,000 years to the dominantly 100,000-year duration of the past half-million years. One of the biggest questions about these changes is whether they were “threshold” responses to a gradual, uniform cooling trend or whether they represent reactions to discrete episodes of cooling. Sosdian and Rosenthal (p. 306) present deep-ocean temperature records from the North Atlantic that show that the cooling happened in distinct steps, at 3 to 2.5 million years ago and at 1.2 to 0.85 million years ago. Combining their record with that of deep ocean water oxygen isotopes allowed the distinction between effects due to global cooling and ice-sheet dynamics. Increases in glacial ice volume and ice-sheet dynamics are implicated in two distinct climate cooling events. Earth has undergone profound changes since the late Pliocene, which led to the development [~2.7 million years ago (Ma)] and intensification (~0.9 Ma) of large-scale Northern Hemisphere ice sheets, recorded as transitions in the benthic foraminiferal oxygen isotope (δ18Ob) record. Here we present an orbitally resolved record of deep ocean temperature derived from benthic foraminiferal magnesium/calcium ratios from the North Atlantic, which shows that temperature variations are a substantial portion of the global δ18Ob signal. The record shows two distinct cooling events associated with the late Pliocene (LPT, 2.5 to 3 Ma) and mid-Pleistocene (MPT, 1.2 to 0.85 Ma) climate transitions. Whereas the LPT increase in ice volume is attributed directly to global cooling, the shift to 100,000-year cycles at the MPT is more likely to be a response to an additional change in ice-sheet dynamics.
Priming in Systemic Plant Immunity

Plants possess inducible systemic defense responses when locally infected by pathogens. Bacterial infection results in the increased accumulation of the mobile metabolite azelaic acid, a nine-carbon dicarboxylic acid, in the vascular sap of Arabidopsis that confers local and systemic resistance against the pathogen Pseudomonas syringae. Azelaic acid primes plants to accumulate salicylic acid (SA), a known defense signal, upon infection. Mutation of the AZELAIC ACID INDUCED 1 (AZI1) gene, which is induced by azelaic acid, results in the specific loss of systemic immunity triggered by pathogen or azelaic acid and of the priming of SA induction in plants. Furthermore, the predicted secreted protein AZI1 is also important for generating vascular sap that confers disease resistance. Thus, azelaic acid and AZI1 are components of plant systemic immunity involved in priming defenses.
Flagellum Mediates Symbiosis

We report here molecular mechanisms underlying a bacteria-archaeon symbiosis. We found that a fermentative bacterium used its flagellum for interaction with a specific methanogenic archaeon. The archaeon perceived a bacterial flagellum protein and activated its metabolism (methanogenesis). Transcriptome analyses showed that a substantial number of genes in the archaeon, including those involved in the methanogenesis pathway, were up-regulated after the contact with the flagellum protein. These findings suggest that the bacterium communicates with the archaeon by using its flagellum.
An efficient cluster-based outdoor user positioning using LTE and WLAN signal strengths

In this paper we propose a novel cluster-based RF fingerprinting method for outdoor user-equipment (UE) positioning using both LTE and WLAN signals. It uses a simple cost effective agglomerative hierarchical clustering with Davies-Bouldin criterion to select the optimal cluster number. The positioning method does not require training signature formation prior to UE position estimation phase. It is capable of reducing the search space for clustering operation by using LTE cell-ID searching criteria. This enables the method to estimate UE positioning in short time with less computational expense. To validate the cluster-based positioning real-time field measurements were collected using readily available cellular mobile handset equipped with Nemo Handy software. Output results of the proposed method were compared with a single grid-cell layout based RF fingerprinting method. Simulation results show that if a single LTE and six WLAN signal strengths are used then the proposed method can improve positioning accuracy of 35% over the grid-based RF fingerprinting.
γ-Secretase Heterogeneity in the Aph1 Subunit: Relevance for Alzheimer’s Disease

Tactical Target Intramembrane proteolysis by the γ-secretase complex is important during development and in the pathology of Alzheimer's disease. γ-Secretase has usually been considered as a homogeneous activity. Serneels et al. (p. 639, published online 19 March; see the Perspective by Golde and Kukar) now show that the Aph1B component of the γ-secretase complex is responsible for the generation of long β-amyloid species involved in Alzheimer's disease. In a mouse model of Alzheimer's disease, full knockout of Aph1B improved disease phenotypes, without the sort of toxicity previously observed when targeting γ-secretase more generally. Targeted knockout of only part of the γ-secretase complex lessens toxicity and still improves disease phenotypes. The γ-secretase complex plays a role in Alzheimer’s disease and cancer progression. The development of clinically useful inhibitors, however, is complicated by the role of the γ-secretase complex in regulated intramembrane proteolysis of Notch and other essential proteins. Different γ-secretase complexes containing different Presenilin or Aph1 protein subunits are present in various tissues. Here we show that these complexes have heterogeneous biochemical and physiological properties. Specific inactivation of the Aph1B γ-secretase in a mouse Alzheimer’s disease model led to improvements of Alzheimer’s disease–relevant phenotypic features without any Notch-related side effects. The Aph1B complex contributes to total γ-secretase activity in the human brain, and thus specific targeting of Aph1B-containing γ-secretase complexes may help generate less toxic therapies for Alzheimer’s disease.
A Comparative Evaluation of New and Conventional Knee Orthoses for Control of Anterior Tibial Displacement

Anterior cruciate ligament deficient knees are a common pathological condition for which a knee orthosis is used. The ability of a custom knee orthosis to prevent anterior displacement of the tibia is of critical importance when used on patients with an anterior cruciate ligament deficient knee. A mechanical test program was carried out to compare a novel orthotic fabrication platform, Composite Reinforcement Instead of Sidebars, with commercially available knee braces. The ability of the knee orthoses to prevent anterior tibial displacement served as the criterion for comparison in the test program. The Composite Reinforcement Instead of Sidebars knee orthoses were found to be the most effective of all braces studied in resisting tibial translation in a surrogate model of the knee. The orthoses were also about twice as effective as the competitive braces on a stiffness/weight basis.
Pattern‐based GUI testing: Bridging the gap between design and quality assurance

Software systems with a graphical user interface (GUI) front end are typically designed using user interface (UI) Patterns, which describe generic solutions (with multiple possible implementations) for recurrent GUI design problems. However, existing testing techniques do not take advantage of this fact to test GUIs more efficiently. In this paper, we present a new pattern‐based GUI testing (PBGT) approach that formalizes the notion of UI Test Patterns, which are generic test strategies to test UI patterns over their different implementations. The PBGT approach is evaluated via 2 case studies. The first study involves 2 fielded Web application subjects; findings show that PBGT is both practical and useful, as testing teams were able to find real bugs in a reasonable time interval. The second study allows deeper analysis by studying software subjects seeded with artificial faults; the findings show that PBGT is more effective than a manual model‐based test case generation approach.
Modulation of human trigeminal and extracranial nociceptive processing by transcranial direct current stimulation of the motor cortex

Objective: The study was conducted to investigate the after-effect of transcranial direct current stimulation (tDCS) applied over the human primary motor cortex (M1) on trigeminal and extracranial nociceptive processing. Basic procedures: Nineteen healthy volunteers were stimulated using cathodal, anodal (both 1 mA) or sham tDCS for 20 minutes. Pain processing was assessed by recording trigeminal and extracranial pain-related evoked potentials (PREPs) following electrical stimulation of the contralateral forehead and hand at baseline, 0, 20 and 50 minutes post-tDCS. Main findings: Cathodal tDCS resulted in decreased peak-to-peak amplitudes (PPAs) by 18% while anodal tDCS lead to increased PPAs of PREPs by 35% (p < .05). Principal conclusions: The decreased PPAs suggest an inhibition and the increased PPAs of PREPs suggest an excitation of trigeminal and extracranial pain processing induced by tDCS of the M1. These results may provide evidence for the effectiveness of tDCS as a therapeutic instrument in treating headache disorders.
Activity aware video collection to minimize resource usage in smart camera nodes

We envision future video sensor networks comprising tether-less smart camera nodes capable of supporting a variety of applications, ranging from video surveillance to traffic management, smart environments to ecological monitoring, etc. A key difference between video sensor networks and traditional multi-camera systems is that the later typically are not concerned with power, storage, and bandwidth usage. Power requirements, especially, must be considered when designing tether-less smart camera networks, since the operational life of a camera node is closely tied to the available power. Video capture and processing performed on a camera node and the communication between nodes needed to carry out collaborative sensing tasks impact power usage of these camera nodes. Therefore, one must devise strategies to minimize video capture and processing at each node and communication between nodes in order to reduce power consumption at each node, thereby increasing the operational life of a video sensor network.
A minimal test practice framework for emerging software organizations

Testing takes a large share of software development efforts, and hence is of interest when seeking improvements. Several test process improvement frameworks exist, but they are extensive and much too large to be effective for smaller organizations. This paper presents a minimal test practice framework (MTPF) that allows the incremental introduction of appropriate practices at the appropriate time in rapidly expanding organizations. The process for introducing the practice framework tries to minimize resistance to change by maximizing the involvement of the entire organization in the improvement effort and ensuring that changes are made in small steps with a low threshold for each step. The practice framework created and its method of introduction have been evaluated at one company by applying the framework for a one‐year period. Twelve local software development companies have also evaluated the framework in a survey. Copyright © 2005 John Wiley & Sons, Ltd.
AMPK Regulates the Circadian Clock by Cryptochrome Phosphorylation and Degradation

Coupling Clocks and Metabolism Circadian clocks in mammals coordinate behavior and physiology with daily light-dark cycles by driving rhythmic transcription of thousands of genes. The master clock in the brain is set by light, but clocks in peripheral tissues, such as the liver, are set by daily feeding. Such coupling should allow tissues to “anticipate” food consumption and optimize the timing of metabolic processes, but how nutritional status is communicated to peripheral clocks is unclear. Studying cell culture models and mice, Lamia et al. (p. 437; see the Perspective by Suter and Schibler) show that the nutrient-responsive signaling molecule AMPK (AMP-activated protein kinase) provides metabolic information to circadian clocks by triggering phosphorylation and subsequent degradation of the clock component cryptochrome-1. Thus—cryptochromes, which originally evolved as blue-light photoreceptors in plants, act as chemical energy sensors in mammals. The protein kinase AMPK couples circadian clocks and metabolism in mammals through effects on a cryptochrome protein. Circadian clocks coordinate behavioral and physiological processes with daily light-dark cycles by driving rhythmic transcription of thousands of genes. Whereas the master clock in the brain is set by light, pacemakers in peripheral organs, such as the liver, are reset by food availability, although the setting, or “entrainment,” mechanisms remain mysterious. Studying mouse fibroblasts, we demonstrated that the nutrient-responsive adenosine monophosphate–activated protein kinase (AMPK) phosphorylates and destabilizes the clock component cryptochrome 1 (CRY1). In mouse livers, AMPK activity and nuclear localization were rhythmic and inversely correlated with CRY1 nuclear protein abundance. Stimulation of AMPK destabilized cryptochromes and altered circadian rhythms, and mice in which the AMPK pathway was genetically disrupted showed alterations in peripheral clocks. Thus, phosphorylation by AMPK enables cryptochrome to transduce nutrient signals to circadian clocks in mammalian peripheral organs.
Mars Water-Ice Clouds and Precipitation

Phoenix Ascending The Phoenix mission landed on Mars in March 2008 with the goal of studying the ice-rich soil of the planet's northern arctic region. Phoenix included a robotic arm, with a camera attached to it, with the capacity to excavate through the soil to the ice layer beneath it, scoop up soil and water ice samples, and deliver them to a combination of other instruments—including a wet chemistry lab and a high-temperature oven combined with a mass spectrometer—for chemical and geological analysis. Using this setup, Smith et al. (p. 58) found a layer of ice at depths of 5 to 15 centimeters, Boynton et al. (p. 61) found evidence for the presence of calcium carbonate in the soil, and Hecht et al. (p. 64) found that most of the soluble chlorine at the surface is in the form of perchlorate. Together these results suggest that the soil at the Phoenix landing site must have suffered alteration through the action of liquid water in geologically the recent past. The analysis revealed an alkaline environment, in contrast to that found by the Mars Exploration Rovers, indicating that many different environments have existed on Mars. Phoenix also carried a lidar, an instrument that sends laser light upward into the atmosphere and detects the light scattered back by clouds and dust. An analysis of the data by Whiteway et al. (p. 68) showed that clouds of ice crystals that precipitated back to the surface formed on a daily basis, providing a mechanism to place ice at the surface. Laser remote sensing from Mars’ surface revealed water-ice clouds that formed during the day and precipitated at night. The light detection and ranging instrument on the Phoenix mission observed water-ice clouds in the atmosphere of Mars that were similar to cirrus clouds on Earth. Fall streaks in the cloud structure traced the precipitation of ice crystals toward the ground. Measurements of atmospheric dust indicated that the planetary boundary layer (PBL) on Mars was well mixed, up to heights of around 4 kilometers, by the summer daytime turbulence and convection. The water-ice clouds were detected at the top of the PBL and near the ground each night in late summer after the air temperature started decreasing. The interpretation is that water vapor mixed upward by daytime turbulence and convection forms ice crystal clouds at night that precipitate back toward the surface.
Dissociable Components of Rule-Guided Behavior Depend on Distinct Medial and Prefrontal Regions

Card Sorting Monkeys Single-neuron studies in primates help to establish a detailed understanding of cognitive processing and to provide an experimental base for understanding the cognitive deficits incurred by patients who have suffered damage to areas of the brain. Buckley et al. (p. 52) present the results of an intensive behavioral analysis of a group of monkeys bearing lesions to distinct areas of the prefrontal lobe. The Wisconsin Card Sorting Task is widely used in the clinic to assess the flexible learning of abstract rules. In the primates, a functional dissociation was observed across three regions: the principal sulcus, the orbitofrontal cortex, and the anterior cingulate cortex. This set of results contributes to the ongoing discussion of goal-directed behavior and serves to bridge neuropsychological studies in human patients and neurophysiological studies in primates. A card-sorting task shows that three distinct regions of the monkey prefrontal cortex perform distinct cognitive functions. Much of our behavior is guided by rules. Although human prefrontal cortex (PFC) and anterior cingulate cortex (ACC) are implicated in implementing rule-guided behavior, the crucial contributions made by different regions within these areas are not yet specified. In an attempt to bridge human neuropsychology and nonhuman primate neurophysiology, we report the effects of circumscribed lesions to macaque orbitofrontal cortex (OFC), principal sulcus (PS), superior dorsolateral PFC, ventrolateral PFC, or ACC sulcus, on separable cognitive components of a Wisconsin Card Sorting Test (WCST) analog. Only the PS lesions impaired maintenance of abstract rules in working memory; only the OFC lesions impaired rapid reward-based updating of representations of rule value; the ACC sulcus lesions impaired active reference to the value of recent choice-outcomes during rule-based decision-making.
Abscisic Acid Inhibits Type 2C Protein Phosphatases via the PYR/PYL Family of START Proteins

ABA Receptor Rumbled? The plant hormone abscisic acid (ABA) is critical for normal development and for mediating plant responses to stressful environmental conditions. Now, two papers present analyses of candidate ABA receptors (see the news story by Pennisi). Ma et al. (p. 1064; published online 30 April) and Park et al. (p. 1068, published online 30 April) used independent strategies to search for proteins that physically interact with ABI family phosphatase components of the ABA response signaling pathway. Both groups identified different members of the same family of proteins, which appear to interact with ABI proteins to form a heterocomplex that can act as the ABA receptor. The variety of both families suggests that the ABA receptor may not be one entity, but rather a class of closely related complexes, which may explain previous difficulties in establishing its identity. Links between two ancient multimember protein families signal responses to the plant hormone abscisic acid. Type 2C protein phosphatases (PP2Cs) are vitally involved in abscisic acid (ABA) signaling. Here, we show that a synthetic growth inhibitor called pyrabactin functions as a selective ABA agonist. Pyrabactin acts through PYRABACTIN RESISTANCE 1 (PYR1), the founding member of a family of START proteins called PYR/PYLs, which are necessary for both pyrabactin and ABA signaling in vivo. We show that ABA binds to PYR1, which in turn binds to and inhibits PP2Cs. We conclude that PYR/PYLs are ABA receptors functioning at the apex of a negative regulatory pathway that controls ABA signaling by inhibiting PP2Cs. Our results illustrate the power of the chemical genetic approach for sidestepping genetic redundancy.
Empirical-Bayesian availability indices of safety and time critical software systems with corrective maintenance

If the recovery or remedial time is not incorporated in the reliability of a software module in a safety and time-critical integrated system operation, then a mere reliability index based on failure characteristics is simply not adequate and realistic. In deriving the probability density function (pdf) of the software availability, empirical Bayesian procedures will be used to employ expert engineering judgment through appropriate noninformative and informative prior distribution functions employing various definitions of risk functions. It is emphasized that the usage of maximum likelihood estimators regardless of the extent of historical data is erroneous and misleading.
Predicting Fatigue Failures

New methods for predicting fatigue may extend the usefulness of materials that actively resist cracking. Engineers who design structures often start at the end: They consider how the materials used will fail. Structures must be overdesigned—a bridge may be able to withstand twice the expected load when it is first built—but over time, repeated cycles of loading and unloading introduce defects in the materials that can ultimately lead to fatigue failure; for example, a paper clip that is bent back and forth until eventually it snaps. Predicting failure is easier for ductile than for brittle materials, and designers can accurately model their response to fatigue loading (1). However, many relatively brittle materials, such as advanced ceramics, intermetallics, and composites of brittle and ductile materials, are seeing increased use due to their favorable low-density or high-temperature properties. New methods are needed to predict when and how these materials will fail due to cyclic fatigue loading.
The Natural History of Sleep Disturbances in Severe Missile Head Injury

Twenty patients who had suffered missile head injuries (MHI) during the Lebanese War were separated into three groups, based on clinical criteria. All the patients were monitored polysomnographically (PSG) 3 and 12 months after the injury. The records were double-blind scored. The clinical and PSG data were compared, and discrepancies were found between the clinical and PSG evaluation of sleep in MHI patients. Sleep disturbance is not an obligatory feature of MHI patients. MHI associated with hypersomnia was found to have a good prognosis. Insomnia is usually associated with long coma and severe diffuse brain lesions in MHI patients and has a much more severe prognosis than hypersomnia in these patients.