Miracle-dz/UniFAR-FTUs huggingface dataset:
Genome-Wide Association Study Uncovers Novel Genomic Regions Associated With Coleoptile Length in Hard Winter Wheat

Successful seedling establishment depends on the optimum depth of seed placement especially in drought-prone conditions, providing an opportunity to exploit subsoil water and increase winter survival in winter wheat. Coleoptile length is a key determinant for the appropriate depth at which seed can be sown. Thus, understanding the genetic basis of coleoptile length is necessary and important for wheat breeding. We conducted a genome-wide association study (GWAS) using a diverse panel of 298 winter wheat genotypes to dissect the genetic architecture of coleoptile length. We identified nine genomic regions associated with the coleoptile length on seven different chromosomes. Of the nine genomic regions, five have been previously reported in various studies, including one mapped to previously known Rht-B1 region. Three novel quantitative trait loci (QTLs), QCL.sdsu-2AS, QCL.sdsu-4BL, and QCL.sdsu-5BL were identified in our study. QCL.sdsu-5BL has a large substitution effect which is comparable to Rht-B1's effect and could be used to compensate for the negative effect of Rht-B1 on coleoptile length. In total, the nine QTLs explained 59% of the total phenotypic variation. Cultivars ‘Agate’ and ‘MT06103’ have the longest coleoptile length and interestingly, have favorable alleles at nine and eight coleoptile loci, respectively. These lines could be a valuable germplasm for longer coleoptile breeding. Gene annotations in the candidate regions revealed several putative proteins of specific interest including cytochrome P450-like, expansins, and phytochrome A. The QTLs for coleoptile length linked to single-nucleotide polymorphism (SNP) markers reported in this study could be employed in marker-assisted breeding for longer coleoptile in wheat. Thus, our study provides valuable insights into the genetic and molecular regulation of the coleoptile length in winter wheat.
KAAS: an automatic genome annotation and pathway reconstruction server

The number of complete and draft genomes is rapidly growing in recent years, and it has become increasingly important to automate the identification of functional properties and biological roles of genes in these genomes. In the KEGG database, genes in complete genomes are annotated with the KEGG orthology (KO) identifiers, or the K numbers, based on the best hit information using Smith–Waterman scores as well as by the manual curation. Each K number represents an ortholog group of genes, and it is directly linked to an object in the KEGG pathway map or the BRITE functional hierarchy. Here, we have developed a web-based server called KAAS (KEGG Automatic Annotation Server: http://www.genome.jp/kegg/kaas/) i.e. an implementation of a rapid method to automatically assign K numbers to genes in the genome, enabling reconstruction of KEGG pathways and BRITE hierarchies. The method is based on sequence similarities, bi-directional best hit information and some heuristics, and has achieved a high degree of accuracy when compared with the manually curated KEGG GENES database.
The continuing decline in South-East Australian rainfall - Update to May 2009

Most of South-Eastern Australia (SEA) has seen reduced rainfall since the late 1990s (National Climate Centre – NCC-, 2008). Murphy and Timbal (2008) (hereafter, MT08) described the ongoing dry conditions across most of southern Australia to 2006 and its many impacts; of particular concern for water resource management agencies have been recent record low inflows or river run-offs into the Murray-Darling Basin (MDBA, 2009).
Dynamic triggering of deep earthquakes within a fossil slab

The 9 November 2009 Mw 7.3 Fiji deep earthquake is the largest event in a region west of the Tonga slab defined by scattered seismicity and velocity anomalies. The main shock rupture was compact, but the aftershocks were distributed along a linear feature at distances of up to 126 km. The aftershocks and some background seismicity define a sharp northern boundary to the zone of outboard earthquakes, extending westward toward the Vitiaz deep earthquake cluster. The northern earthquake lineament is geometrically similar to tectonic reconstructions of the relict Vitiaz subduction zone at 8–10 Ma, suggesting the earthquakes are occurring in the final portion of the slab subducted at the now inactive Vitiaz trench. A Coulomb stress change calculation suggests many of the aftershocks were dynamically triggered. We propose that fossil slabs contain material that is too warm for earthquake nucleation but may be near the critical stress susceptible to dynamic triggering.
Behind Closed Doors: Violence in the American Family

PART ONE: THE ISSUES Violence in the Home PART TWO: THE VIOLENT FAMILY The Marriage License as a Hitting License Spare the Rod? Kids Will Be Kids Violence Between Brothers and Sisters PART THREE: SOCIAL PATTERNS IN FAMILY VIOLENCE The Social Heredity of Family Violence Who Are the Violent Americans? PART FOUR: SOME IMMEDIATE CAUSES Marital Conflict and Marital Violence Violent Families Children, Stress, and Power PART FIVE: THE FUTURE The Social Causes of Family Violence Putting the Pieces Together Toward Reducing Family Violence Band-Aids, Ambulances, and Solutions
An Efficient Cluster Algorithm for CP(N-1) Models

We construct an efficient cluster algorithm for ferromagnetic SU(N)-symmetric quantum spin systems. Such systems provide a new regularization for CP(N-1) models in the framework of D-theory, which is an alternative non-perturbative approach to quantum field theory formulated in terms of discrete quantum variables instead of classical fields. Despite several attempts, no efficient cluster algorithm has been constructed for CP(N-1) models in the standard formulation of lattice field theory. In fact, there is even a no-go theorem that prevents the construction of an efficient Wolff-type embedding algorithm. We present various simulations for different correlation lengths, couplings and lattice sizes. We have simulated correlation lengths up to 250 lattice spacings on lattices as large as 640x640 and we detect no evidence for critical slowing down.
Traditional Agrarian Landscape in the Mediterranean Mountains. A Regional and Local Factor Analysis in the Central Spanish Pyrenees

Development of rural areas needs information about sustainable use of the land. The main objective of this research is to study the spatial distribution pattern of different field types in the traditional agricultural landscape in the Central Spanish Pyrenees (flat fields, four different terrace fields, sloping field and shifting agriculture) related to different geoecological variables: slope, exposition, altitude, distance to the villages, rainfall (intensity and volume), lithology and demographic pressure. Agricultural land patterns were mapped in five valleys in the Central Pyrenees from aerial photographs (1957). These maps were digitised and implemented in a Geographic Information System on a scale 1:50,000. We determined the influence of different geoecological variables in the spatial distribution of land agricultural patterns at local and regional valley using statistical analysis. The results showed that the agricultural area occupied a large extension, despite physical environment limitations, extending even in marginal slopes, with little agricultural skills, creating a complex landscape with different field patterns. At the local scale (valley), slope and distance are the more influence variables to explain the spatial distribution of the different field types. At the regional scale, in the Western valleys, sloping fields and shifting agriculture predominate, while terraces dominate in the Eastern valleys. Distance to the village and rainfall intensity is the more determinant factors in the spatial distribution. Copyright © 2017 John Wiley & Sons, Ltd.
Dissipative Particle Dynamics Simulations of Self-Assemblies of Liposomes for Drug Delivery Applications

Liposomes are essential components in the development of functional materials for drug delivery; this is mainly due to its ability to self-associate spontaneously and form bilayer vesicles. In these potential applications, knowing the size of selfassembled liposomes is essential for optimal performance; however, this process still has many unanswered questions. Conventional experimental techniques to study self-assemblies of liposome nanoparticles still have a great challenge. Computational simulations emerge as an alternative to understand the role of thermodynamic properties responsible for the self-assembly, particularly when they are unreachable experimentally because of limited time and length resolutions. In this chapter, we present the advantages and disadvantages of dissipative particle dynamic method to explore the functioning of liposome self-assembly in the transport of drugs.
Proposed association between the hexanucleotide repeat of C9orf72 and opposability index of the thumb

Objective : Amyotrophic lateral sclerosis (ALS) is a fatal disease caused by motor neuron and sub-cerebral projection neuron degeneration. We sought to explore the particular susceptibility of humans to neurodegeneration and whether any characteristic human features might predispose to selective vulnerability of the critical motor circuitry in ALS. The pathophysiology of the C9orf72 repeat is not yet understood, despite its role as a common cause of ALS and frontotemporal dementia. Methods : We examined the development of the monosynaptic cortico-motoneuronal system, key to skilled hand movements, measured by the thumb opposability index, and its relationship to the C9orf72 hexanucleotide repeat expansion, a strong predisposing factor for neurodegeneration, using the genomic tool BLAST. Results : We found a statistically significant linear relationship between the C9orf72 hexanucleotide bit score, a measure of genomic conservation of the aligned region across different species, and the thumb opposability index (Pearson’s correlation coefficient of 0.78, p value0.023). The C9orf72 hexanucleotide repeat was only found in humans, chimpanzees and gorillas, species with higher opposability indices. Conclusions : This may support a role of the hexanucleotide repeat in the same developmental pathways in species with higher prehensility, which may be associated with the selective vulnerability of corticomotoneuronal cells in humans, manifested most obviously as the ‘split hand’ syndrome in ALS.
Engineering Applications of Artificial Intelligence

Supply chains have been impacted by the COVID-19 pandemic, which is the most recent worldwide disaster. After the world health organization recognized the latest phenomena as a pandemic, nations became incapacitated to provide the required medical supplies. In the current situation, the world seeks an essential solution for COVID-19 Pandemic Wastes (CPWs) by pushing the pandemic to a stable condition. In this study, the development of a supply chain network is contrived for CPWs utilizing optimization modeling tools. Also, an IoT platform is devised to enable the proposed model to retrieve real-time data from IoT devices and set them as the model’s inputs. Moreover, sustainability aspects are appended to the proposed IoT-enabled model considering its triplet pillars as objective functions. A real case of Puebla city and 15 experiments are used to validate the model. Furthermore, a combination of metaheuristic algorithms utilized to solve the model and also seven evaluation indicators endorse the selection of efficient solution approaches. The evaluation indicators are appointed as the inputs of statistical and multicriteria decision-making hybridization to prioritize the algorithms. The result of the Entropy Weights method and Combined Compromise Solution approach confirms that MOGWO has better performance for the medium-sizes, case study and an overall view. Also, NSHHO outclasses the small-size and large-size experiments.
Engineering Applications of Artificial Intelligence

In recent years generative design techniques have become firmly established in numerous applied fields, especially in engineering. These methods are crucial for automating the initial stages of the engineering design of various structures, which reduces the amount of routine work. However, existing approaches are limited by the specificity of the problem under consideration. In addition, they do not provide the desired flexibility in choosing a method for a particular problem. To avoid these issues, we proposed a general approach to an arbitrary generative design problem and implemented a novel open-source framework called GEFEST (Generative Evolution For Encoded STructure) on its basis. This approach is based on three general principles: sampling, estimation, and optimization. This ensures the freedom of method adjustment for the solution of the particular generative design problem and therefore enables the construction of the most suitable one. A series of experimental studies was conducted to confirm the effectiveness of the GEFEST framework. It involved synthetic and real-world cases (coastal engineering, microfluidics, thermodynamics, and oil field planning). The flexible structure of GEFEST makes it possible to obtain results that surpass baseline and state-of-the-art solutions: 12% improvement in the coastal engineering problem; 9% in microfluidics; 8% in thermodynamics and 7% in oil field planning.
Ultrasound-guided erector spinae plane block versus port site infiltration for postoperative pain and quality of recovery in adult patients undergoing laparoscopic cholecystectomy: An assessor-blinded randomised controlled trial

Background and Aim: Pain following laparoscopic cholecystectomy (LC) is common and results in poor quality of recovery. Our study aimed to compare the analgesic efficacy of port site local infiltration, novel erector spinae plane (ESP) block, and standard regimen in patients undergoing LC and its impact on functional recovery. Methods: After ethical approval and registering the trial, we randomly allocated 105 adult patients undergoing LC to three groups: Group I (n = 35), received multimodal analgesia; Group II (n = 35), received pre-incisional port site infiltration with 20 ml of 0.375% bupivacaine; and Group III (n = 35), preoperative bilateral ESP block with 20 ml of 0.375% bupivacaine bilaterally was administered. Pain severity, fentanyl consumption, and time to first rescue analgesia were recorded over 24 h. Quality of recovery (QoR-15) was assessed at baseline and 24 h postoperatively. Results: Pain in the first 6 h was lowest in the ESP group (P < 0.001). Although static pain in the infiltration group was comparable with that in the ESP group after 6 h (P > 0.05), dynamic pain was better in the ESP group till 20 h postoperatively (P < 0.05). Fentanyl consumption was significantly lower in the ESP group (P < 0.001). Global and sub-dimensional QoR-15 scores were significantly higher only in the ESP group at 24 h compared to the other two groups (P < 0.001). The infiltration group did better than the control group in terms of total opioid requirement (P < 0.001) and Visual Analogue Scale (VAS) score after 6 h (P < 0.001). Conclusion: ESP block provided lower postoperative pain scores with opioid-sparing and better quality of recovery in patients undergoing LC.
Ultrasound guided erector spinae plane block versus intrathecal morphine for analgesia following major hepatopancreaticobiliary surgery

ABSTRACT Background Intrathecal morphine (ITM) has been evidenced to provide efficient analgesia for hepatopancreaticobiliary surgery (HPB) in the postoperative period. Despite its benefits, ITM carries certain risks, such as pruritus, postoperative nausea and vomiting, and of utmost importance, the possibility of delayed respiratory depression. We conducted this study to compare the effectiveness of bilateral erector spinae plane block (ESPB) and ITM for analgesia following major HPB surgery. Our hypothesis was that bilateral ESPB would lead to a significant reduction in opioid consumption within the first 24 hours following surgery, with a lower incidence of side effects. Methods Forty patients with scheduled major HPB surgery were randomly allocated to receive either bilateral ESPB (n = 20) or ITM (n = 20) before general anesthesia induction. The primary outcome was cumulative postoperative nalbuphine consumption in the first 24 hours. Results Cumulative nalbuphine consumption at 24 hours after surgery was significantly lower in the ITM group compared to ESPB (3.05 ± 0.38 versus 6.56 ± 0.88 respectively). However, the ESPB group demonstrated effective pain control as indicated by pain scores of ≤2 at rest and ≤3 when coughing throughout all measured time points. Moreover, ESPB significantly reduced the incidence of postoperative nausea, vomiting (p = 0.03), and pruritus (p = 0.003) within the first 24 hours postoperatively compared to ITM. Conclusions Although bilateral ESPB resulted in higher opioid consumption than ITM in the first 24 hours after major HPB surgery, the adverse effects were less with minimal or no risk of hemodynamic instability.
Walking the Tightrope: Communicative Tensions in Disenfranchised Grief Among Families Managing Substance Use Disorder

ABSTRACT This study investigates the communicative tensions inherent to the experience of disenfranchised grief among family members of individuals with substance use disorder (SUD). In the context of a family member with SUD, 98 adult-affected family members (AFMs) described their struggles with disenfranchised grief, a form of grief characterized by deprivation of support or recognition from others. The results of a deductive, qualitative analysis guided by relational dialectics theory (RDT; Baxter & Montgomery, 1996) indicated that AFMs traverse the dialectical poles of integration-separation, stability-change, and expression-non-expression both within the relationship (internally) and with those “on the outside” (externally). Additionally, AFMs grappled with a tension cited in previous work examining contradictions among spouses managing adult dementia: presence-absence (Baxter etal., 2002). The findings (a) illuminate the disenfranchised grief experienced by AFMs, (b) unpack the interactional implications of this unique form of suffering by situating disenfranchised grief as a communicative phenomenon, and (c) call for increased social and clinical support for AFMs experiencing disenfranchised grief.
On the Horizon

made systems much more vulnerable to malicious attacks that can have far-reaching implications on our daily lives. The catastrophic failure of AT&T’s telecommunication network in New York City, for example, which affected both airline reservation and American Red Cross blood-supply-tracking systems, and the Code Red worm, which exploited a buffer overflow in Internet Information Service (IIS), indicate a rising problem with computer and system security. Traditionally, system security has meant access control and cryptography support, but the Internet’s phenomenal growth has led to the large-scale adoption of networked computer systems for a diverse cross section of applications with highly varying requirements. In this all-pervasive computing environment, the need for security and reliability has expanded from a few expensive systems to a basic computing necessity. This new paradigm has important consequences:
Valvular Heart Disease: Focus on Women

Calcific aortic stenosis is a disease of the elderly and aortic valve replacement should always be considered for severe symptomatic disease; comorbidities, not age, determine surgical risk. Aortic regurgitation imposes a pressure and volume load on the left ventricle so that close monitoring is needed to identify patients at risk for irreversible left ventricular dysfunction, although symptoms are the most common indication for valve replacement. Early intervention now is recommended for rheumatic mitral stenosis due to the effectiveness of percutaneous balloon valvotomy. Earlier intervention also may be considered in selected patients with mitral regurgitation at experienced centers when valve anatomy is favorable for a successful repair. Semiquantitative descriptors of regurgitation as mild, moderate, or severe are no longer adequate; management of adults with chronic valve disease requires quantitation of both the severity of valve disease and of left ventricular size and systolic function.
UvA-DARE ( Digital Academic Repository ) Microcirculatory dysfunction in critically ill patients : prevalence and significance from a bedside perspective

Introduction Persisting microcirculatory alterations in severe sepsis and septic shock are known to be associated with increased morbidity and mortality. These alterations occur despite optimal macrohemodynamic resuscitation. Therefore, specific pro-microcirculatory strategies may improve oxygen delivery to the cells. Therapies intended to ameliorate microcirculatory alterations have yielded inconsistent results this far. Ketanserin, a serotonin receptor antagonist (5HT2a), is an attractive candidate, because of its vasodilatory, antithrombotic and anti-inflammatory effects. Methods This study is an open label pilot study on the effect of stepwise increased ketanserin administration on persisting sublingual microcirculatory alterations in severe sepsis/ septic shock. Persisting microcirculatory alterations were defined as a small vessel (<20 μm) microvascular flow index (MFI) ≤ 2.5 after a strict macrohemodynamic resuscitation protocol. Sidestream Dark Field imaging (SDF) was applied to assess the microcirculation. Starting dose was a bolus of 0.015 mg/kg followed by a 30 minute continuous ketanserin infusion of 0.03 mg/kg/hour. The dose was increased every 30 minutes (maximum study duration 2 hours) until a small vessel MFI>2.9, the primary endpoint, was observed. Secondary endpoint was the incidence of refractory hypotension (MAP <50 mmHg > 5 minutes despite ongoing resuscitation). Results Ten patients with APACHE IV 115 [100-136] (median [IQR]), SOFA 11 [8-14] and an ICU mortality of 50% were included. Baseline small vessel MFI was 1.71 [1.31-2.32], significantly increasing to 2.96 [2.54-3.00] (P=0.021) during the ketanserin infusion. The total ketanserin dose was 0.09 [0.08-0.13] mg/kg per patient in 60 [30-60] minutes. In 3 patients (30%) the ketanserin infusion was discontinued due to refractory hypotension. Overall, central/mixed venous oxygen saturation increased and central-to-toe temperature gradient decreased, whereas lactate levels and cardiac index remained stable during the ketanserin infusion. Conclusion In this open label pilot study, an improvement in microcirculatory perfusion was observed during ketanserin administration in patients with severe sepsis and septic shock after macrohemodynamic resuscitation. This finding needs further exploration in a placebocontrolled setting. Trial registration: NCT01329887 7 123 Effects of ketanserin on microcirculatory alterations in sepsis |