Text Indexing for Long Patterns: Anchors are All you Need

PVLDB Artifact Availability: The source code, data, and/or other artifacts have been made available at https://github.com/lorrainea/BDA- index.Copyright © 2023 the owner/author(s). In many real-world database systems, a large fraction of the data is represented by strings: sequences of letters over some alphabet. This is because strings can easily encode data arising from different sources. It is often crucial to represent such string datasets in a compact form but also to simultaneously enable fast pattern matching queries. This is the classic text indexing problem. The four absolute measures anyone should pay attention to when designing or implementing a text index are: (i) index space; (ii) query time; (iii) construction space; and (iv) construction time. Unfortunately, however, most (if not all) widely-used indexes (e.g., suffix tree, suffix array, or their compressed counterparts) are not optimized for all four measures simultaneously, as it is difficult to have the best of all four worlds. Here, we take an important step in this direction by showing that text indexing with locally consistent anchors (lc-anchors) offers remarkably good performance in all four measures, when we have at hand a lower bound l on the length of the queried patterns --- which is arguably a quite reasonable assumption in practical applications. Specifically, we improve on the construction of the index proposed by Loukides and Pissis, which is based on bidirectional string anchors (bd-anchors), a new type of lc-anchors, by: (i) designing an average-case linear-time algorithm to compute bd-anchors; and (ii) developing a semi-external-memory implementation to construct the index in small space using near-optimal work. We then present an extensive experimental evaluation, based on the four measures, using real benchmark datasets. The results show that, for long patterns, the index constructed using our improved algorithms compares favorably to all classic indexes: (compressed) suffix tree; (compressed) suffix array; and the FM-index.European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreements No 872539 and 956229, respectively; and by UKRI through REPHRAIN (EP/V011189/1)

A Numerical Model for the Flow Within the Tower of a Tornado- Type Wind Energy System

Introduction Yen proposed the tornado-type wind system to utilize the presure drop created by an intense vortex generated in a vortex chamber [1], The chamber, known as the tower, is used as a low pressure exhaust at the turbine exit. As the surrounding air enters the stationary tower, it generates the vortex. An accurate estimate of the pressure distribution within the tower is required to calculate the maximum power output from a given system. Loth [2] calculated Betz-type limits for different vortextype wind energy systems. For the tornado-type system, he calculated the total pressure drop within the tower based on a flow with solid body rotation within the vortex core of radius a, an inviscid irrotational vortex outside the core and an axial flow of uniform velocity superimposed on the core flow. The turbine exit diameter was limited to that of the core. Although the results showed that the maximum power coefficient, based on the tower's projected area, occurred at the core-to-tower diameter raito of 2aID = 1, Loth [2] expected that for a real vortex the optimum performance may occur when 2a/D = 0.25. Neither the interaction of the axial flow through the turbine nor that of the radial flow from the side boundary with the vortex was considered. The core radius appeard to be a key parameter for estimating the possible power output. Note that for a turbulent vortex flow, the core radius is a function of both local and convecting flow conditions. The variations of the core radius within the vortex boundary layer formed on the flat portion of the tower bottom were shown by using the two-equation turbulence model by Ayad [3] and the second-order closure by Lewellen, et al. [4], Yen tested models of a tornado-type wind syste

Association of Circulating MicroRNA-142-3p with Graves Disease

تهدف هذه الدراسة الى التحري عن وجود دور محتمل للحامض النووي الرايبي الدقيق(miR-142-3p) في ظهور مرض اعتلال الغدةالدرقية المفرط (Graves disease ) وعلاقته مع افراز الاجسام المضادة لمستقبلات الهرمون المحفز للدرقية ( TSHR-Ab )تضمنتالدراسة اخذ عينات دم من اربعين مريضا يعانون من مرض اعتلال الغدة الدرقية المفرط وكانت نتيجة فحص وجود الاجسام المضادة لديهم(TSHR-Ab) موجبة. تم تقسيم المرضى الى مجموعتين (22 مريضا دون علاج و 18 مريضا يأخذ علاج) بالاضافة الى اربعين شخصا منالاصحاء كمجموعة ضابطة. جميع المرضى والاصحاء لايعانون من اي من امراض المناعة الذاتية. تم قياس مستوى تعبير (miR-142-3p)باستخدام تقنية (RT-PCR ). اظهرت النتائج ان هناك زيادة معنوية (p < 0.01 ) في تعبير) miR-142-3p) في مصل دم كل منمجموعتي المرضى مقارنة بالمجموعة الضابطة وفي المرضى الذين يكون لديهم وراثة بالعائلة مقارنة بالذين لم يكن لديهم. بينما كان الفرق فيمستوى تعبير ) miR-142-3p) غير معنوي ( p >0.05 ) بين مجموعتي المرضى. كما اظهرت النتائج ان هناك علاقة موجبة بين مستوىتعبير ) miR-142-3p) مع تركيز الاجسام المضادة (TSHR-Ab ) FT3 ,وFT4, بالاضافة الى ان هذا الحامض النووي الرايبي له قيمةتشخيصية دقيقة ذات حساسية (83%) وخصوصية (80%).نستنتج من هذه الدراسة ان الاختلاف في مستوى تعبير ) miR-142-3p) بينمرضى اعتلال الغدة الدرقية المفرط والاصحاء جعلته ذا قيمة تشخيصية جيدة و من علاقته الموجبة مع تركيز الاجسام المضادة ((TSHR-Ab نستنتجThis study aims to investigate the possible role of circulating microRNA-142-3p (miR-142-3p) in thedevelopment of graves disease (GD) and its association with the antibody directed against thyroidstimulating hormone receptor (TSHR-Ab) production in patients with GD. Forty patients with positiveTSHR-Ab enrolled in this study were divided ,based on treatment, into (22 untreated (newly diagnosed) and18 treated patients) and based on family history (30 with positive family history and 10 with negative familyhistory). In addition to forty healthy subjects with sex and age matching as a control group. The expressionlevel of circulating miR-142-3p was determined by two steps reverse transcription polymerase chain reaction(RT-PCR) technique. Results show that there is a significant elevation (p < 0.01) in the expression of miR-142-3p in the serum of both treated and untreated patients compared with controls and in patients withpositive family history compared with negative family history. While its expression is non-significantlylower (P > 0.05) in the serum of treated patients compared with untreated ones. It has been found that miR-142-3p expression was positively correlated with levels of TSHR-Ab, FT3, and FT4. In addition, the miR-142-3p expression has a good diagnostic accuracy with sensitivity (82%) and specificity (80%). Inconclusion, the differential expression of miR-142-3p between patients and healthy controls appears as apotential biomarker for diagnosis of GD and the positive correlation of miR-142-3p with TSHR-Absuggesting the contribution of this miRNA in the development of GD

The Cleo III Ring Imaging Cherenkov Detector

The CLEO detector has been upgraded to include a state of the art particle identification system, based on the Ring Imaging Cherenkov Detector (RICH) technology, in order to take data at the upgraded CESR electron positron collider. The expected performance is reviewed, as well as the preliminary results from an engineering run during the first few months of operation of the CLEO III detector.Comment: 5 pages, 2 Figures Talk given by M. Artuso at 8th Pisa Meeting on Advanced Detectors, May 200

First report of early blight caused by Alternaria protenta on potato in Algeria

Potato (Solanum tuberosum L.) is one of the most important vegetable crop grown in Algeria. Although less studied than late blight, early blight caused by large-spored Alternaria species including A. solani, and A. grandis is an important foliar disease on these crops under Algerian climatic conditions. Over the past few years, this disease became a major constraint on potato production in Algeria and high incidences of early blight (up to 80 %) were recorded in the north-western parts of Algeria (Bessadat et al., 2016). During years 2012-2014, surveys were carried out and sampling was performed in 12 potato growing regions from East to West and from North to South of Algeria. Two hundred and forty-seven samples with typical early blight symptoms (dark, elongated or circular lesions with concentric rings surrounded by a yellow halo) were collected. Two to three lesions perleaf were excised, surface disinfested for 2 min in 0.1% (v/v) sodium hypochlorite solution and plated on potato dextrose agar medium at 22°C. Twenty-two pure cultures were induced to sporulate by plating on V8 medium and incubating for two weeks under alternating 12 h darkness and 12 h near UV light. Cultural and morphological characteristics of the isolates [color and pigmentation of the culture, shape and size of the conidia (conidial length and width, beak length)] compared with those in the literature (Simmons, 2007) did not clearly differentiate between the large-spored Alternaria species currently reported on potato crops. For identification at the species level, partial regions of the calmodulin (cal) and RNA polymerase second largest subunit (rpb2) genes were amplified using published primer sets (Gannibal et al., 2014; Woudenberg et al., 2014) and sequenced. Maximum likelihood cluster analyses of the resulting nucleotide sequences revealed two isolates (AD82 and AD86 isolated from potato samples collected in the El Oued region) with sequences at the two loci [GenBank accession Nos. KX870505 and KX870506 (cal locus), KX870507 and KX870508 (rpb2 locus)] that shared 100% sequence homology to A. protenta isolate CBS 116696 (KJ718394, JQ646236) and were thus assigned to this species. A. protenta was previously known in Africa only on Helianthus annuus (Simmons, 1986) but isolates from S. tuberosum and S. lycopersicum collected in New Zealand and USA and formerly recognized as A. solani, were recently moved to A. protenta based on phylogeny (Woudenberg et al., 2014). To confirm pathogenicity of the two A. protenta isolates, leaves of susceptible 3-week-old potato plants were inoculated with two 10 µL drops of a 104 conidia/ml suspension. All leaves inoculated with A. protenta showed extending lesions that may reach up 50% of the leaf area at 21 dpi. To our knowledge, we report the first occurrence of A. protenta as pathogen on potato in Algeria.

The Effect of Organic Matter Application on Phosphorus Status in the Calcareous Soil

A field experiment is conducted to study the effect of different levels of peat (0, 25, 50, 75, and 100 Mg ha-1 to uncropped and cropped soil to wheat. Soil samples are taken in different period of time (0, 3, 30, 60, 90, 120, and 180 days after cultivation to determine (NaHCO3-Exteractable P at 3 different depths (0-10, 10-20, and 20-30 cm). Field Experiment is conducted in a randomized complete block design (RCBD) with four replicates. Wheat, Al-Rasheed variety, is cultivated as a testing crop. The entire field is equally dived in two divisions. One of the two divisions is cultivated to wheat and the second is left uncropped. The effect of five levels of peat namely 0, 25, 50, 75, 100 Mg ha-1 is investigated. Soils are fully analyzed to determine its physical and chemical characteristics. The soil samples are collected after 3, 30, 60, 90, 120, and 180 days for determining essential parameters and indicators that reflect the effect of the level of peat applications. Sodium bicarbonate - extractable P in uncropped and cropped soils at all depths, markedly decreases with time after peat application which has been attributed to plant uptake and rapid reaction of P with soil constituents. Sodium bicarbonate - extractable P with time in soil receiving 50 Mg ha-1 in both uncropped and cropped soil linearly decreases with the time of cultivatio