Genome Sequencing of the Sweetpotato Whitefly \u3cem\u3eBemisia tabaci\u3c/em\u3e MED/Q

The sweetpotato whitefly Bemisia tabaci is a highly destructive agricultural and ornamental crop pest. It damages host plants through both phloem feeding and vectoring plant pathogens. Introductions of B. tabaci are difficult to quarantine and eradicate because of its high reproductive rates, broad host plant range, and insecticide resistance. A total of 791 Gb of raw DNA sequence from whole genome shotgun sequencing, and 13 BAC pooling libraries were generated by Illumina sequencing using different combinations of mate-pair and pair-end libraries. Assembly gave a final genome with a scaffold N50 of 437 kb, and a total length of 658 Mb. Annotation of repetitive elements and coding regions resulted in 265.0 Mb TEs (40.3%) and 20 786 protein-coding genes with putative gene family expansions, respectively. Phylogenetic analysis based on orthologs across 14 arthropod taxa suggested that MED/Q is clustered into a hemipteran clade containing A. pisum and is a sister lineage to a clade containing both R. prolixus and N. lugens. Genome completeness, as estimated using the CEGMA and Benchmarking Universal Single-Copy Orthologs pipelines, reached 96% and 79%. These MED/Q genomic resources lay a foundation for future \u27pan-genomic\u27 comparisons of invasive vs. noninvasive, invasive vs. invasive, and native vs. exotic Bemisia, which, in return, will open up new avenues of investigation into whitefly biology, evolution, and management

Exploring the Conformational Transitions of Biomolecular Systems Using a Simple Two-State Anisotropic Network Model

Biomolecular conformational transitions are essential to biological functions. Most experimental methods report on the long-lived functional states of biomolecules, but information about the transition pathways between these stable states is generally scarce. Such transitions involve short-lived conformational states that are difficult to detect experimentally. For this reason, computational methods are needed to produce plausible hypothetical transition pathways that can then be probed experimentally. Here we propose a simple and computationally efficient method, called ANMPathway, for constructing a physically reasonable pathway between two endpoints of a conformational transition. We adopt a coarse-grained representation of the protein and construct a two-state potential by combining two elastic network models (ENMs) representative of the experimental structures resolved for the endpoints. The two-state potential has a cusp hypersurface in the configuration space where the energies from both the ENMs are equal. We first search for the minimum energy structure on the cusp hypersurface and then treat it as the transition state. The continuous pathway is subsequently constructed by following the steepest descent energy minimization trajectories starting from the transition state on each side of the cusp hypersurface. Application to several systems of broad biological interest such as adenylate kinase, ATP-driven calcium pump SERCA, leucine transporter and glutamate transporter shows that ANMPathway yields results in good agreement with those from other similar methods and with data obtained from all-atom molecular dynamics simulations, in support of the utility of this simple and efficient approach. Notably the method provides experimentally testable predictions, including the formation of non-native contacts during the transition which we were able to detect in two of the systems we studied. An open-access web server has been created to deliver ANMPathway results. © 2014 Das et al

Solving a tactical operating room planning problem by a column-generation-based heuristic procedure with four criteria

In some hospitals, an “open scheduling” strategy is applied to solve the operating room planning problem; i.e., surgeons can choose any workday for his surgical cases, and the staffing of anesthetists and nurses is adjusted to maximize the efficiency of operating room utilization. In this paper, we aim at obtaining an efficient operating program for an operating theatre with several multifunctional operating rooms by using this “open scheduling” strategy. First, a mathematical model is constructed to assign surgical cases to operating rooms within one week. This model complies with the availability of operating rooms and surgeons, and its objective is not only to maximize utilization of operating rooms, but to minimize their overtime cost. Then a column-generation-based heuristic (CGBH) procedure is proposed, where four different criteria are compared with each other so as to find a solution with the best performance. In addition, the best approximate solution, obtained by this CGBH procedure after running all the criteria proposed, is compared with the lower bound obtained by an explicit column generation (CG) procedure, LP, to evaluate the distance between the approximate solution obtained and the optimum one. Although no criterion, according to the experimental results, is found superior to all other three in both robustness and quality of the solution obtained, it is found that the best solution obtained among those four criteria is often very close to LP, which means that the proposed algorithm can obtain a near optimal solution. In one word, the CGBH procedure proposed in this paper can obtain an efficient assignment of the surgical cases if the other resources (anesthesia and nursing staff, equipment, beds in the recovery room and etc.) are well organized

Arquatopotamon jizushanense Chu, Zhou & Sun, 2017, sp. n.

<i>Arquatopotamon jizushanense</i> sp. n. <p>(FigS. 1–6)</p> <p> <b>Material examined.</b> Holotype: male (adult), 19.4 × 16.4 mm, NNU 160506, Shiqian Village (25°56’15’’ N, 100°24’19’’ E, 1778 m aSl), JizuShan Town, Binchuan County, Dali City in Yunnan ProVince, coll. Kelin Chu, Pengfei Wang & Hongying Sun, 2 May 2016. ParatypeS: female (adult), 22.3 × 18.5 mm, NNU 160510, Same data aS holotype (allotype); 2 maleS (adult), 20.1 × 16.6 mm, NNU 160507; 18.3 × 15.5 mm, NNU 0 90808, Same data aS holotype.</p> <p> <b>Diagnosis.</b> AS for genuS.</p> <p> <b>Description.</b> Carapace about 1.2 timeS broader than long, Subquadrate, flat, dorSal Surface gently conVeX longitudinally, punctate, glabrouS; regionS diStinctly defined; epibranchial region rugoSe, meSogaStric region Slightly conVeX (Fig. 1 A). CerVical grooVe Shallow, H-Shaped grooVe between gaStric and cardiac regionS diStinct (Fig. 1 A). PoStfrontal lobe Slightly conVeX, poStorbital creSt indiStinct, poStorbital region Slight concaVe (Fig. 1 A, B). Frontal region defleXed downwardS, anterior border emarginated medially (Fig. 1 B). DorSal orbital margin ridged, eXternal orbital angle triangular, outer margin lined with 4 Small granuleS (Fig. 1 B). Anterolateral margin criState, epibranchial tooth pointed, diStinct, clearly demarcated from eXternal orbital tooth (Fig. 1 A).</p> <p>Third maXilliped meruS about 1.1 timeS aS broad aS long, trapezoidal, with median depreSSion, tip of the meruS triangular Shaped; iSchium about 1.4 timeS aS long aS broad, rectangular, with diStinct median SulcuS; eXopod reaching proXimal 1/4 of meruS length, without flagellum (Fig. 1 B, 2B).</p> <p>ChelipedS Slightly unequal; meruS trigonal in croSS-Section; marginS crenulated, carpuS with Sharp Spine on inner diStal angle, with Spinule at baSe (Fig. 1 A, C, 2A). Outer SurfaceS of manuS of major chela Smooth, about 1.5 timeS aS long aS high, Slightly longer than moVable finger, gape narrow when fingerS cloSed, cutting edge lined with rounded, blunt teeth, diStal part of cutting edge Sharp and without teeth (Fig. 1 C, 2A). Ambulatory legS Slender, SurfaceS Smooth; dactyluS Slender, with denSe Spinule, Second ambulatory leg meruS about 1.5 timeS aS long aS dactyluS; laSt leg with propoduS about 1.4 timeS aS long aS broad, Slightly Shorter than dactyluS (Fig. 1 A).</p> <p> Male abdomen broadly triangular, third Somite wideSt; SiXth Somite width 2.2 timeS length, telSon broadly triangular, with about 1.6 timeS aS broad aS long (Fig. 1 C, 3B). Male thoracic Sternum Smooth; median grooVe of male thoracic Sternum deep; interruption between SutureS of SterniteS 4/5, 5/6, 6/7 broad; median longitudinal Suture between SterniteS 7 and 8 moderately long (Fig. 3 A). G1 long, diStal part of Subterminal, terminal Segment arch Shaped (meSioVentral View; Fig. 2 E), tip of terminal Segment reaching Suture between thoracic SterniteS 4/ 5 <i>in</i> situ (Fig. 3 A); Subterminal Segment about 1.9 timeS aS long aS terminal Segment; terminal Segment tongue-Shaped, diStinctly curVed Ventrally (Ventral View) (Fig. 2 D, E, F and G). G2 Slightly longer than G1, baSal Segment about 2.6 timeS aS long aS diStal Segment (Fig. 2 C).</p> <p> Female abdomen longitudinally elongated, oVate; SiXth Somite about 3.3 timeS aS broad aS long, telSon Semicircular, about 2.4 timeS aS broad aS long (Fig. 3 D). Female gonopore on thoracic SterniteS 5/6, reaching Suture between thoracic SterniteS 4/ 5 <i>in</i> situ, deep, without operculum, poSterior margin with V-Shaped notch, anterior portion with protuberance (Fig. 3 C, D). The poSteromedial of female gonopore with domed protuberance on thoracic Sternite 6 (Fig. 3 C, D).</p> <p> <b>Distribution and habitat</b>. <i>Arquatopotamon jizushanense</i> <b>gen. n</b>., <b>sp. n.</b> waS found under StoneS in Small hill StreamS in Shiqian Village (25°56’15’’ N, 100°24’19’’ E), JizuShan Town, Binchuan County, Dali City in Yunnan ProVince, China (Fig. 5 A, B); at an altitude of 1778 m. No other potamidS were obSerVed at the type locality.</p> <p> <b>Live coloration.</b> Carapace iS uSually dark brown, whereaS chelipedS and ambulatory legS are reddiSh brown to purple in life (Fig. 5 B).</p> <p> <b>Etymology.</b> <i>Arquatopotamon jizushanense</i> <b>gen. n</b>., <b>sp. n.</b> iS named after the type locality, JizuShan Town in Yunnan ProVince, China.</p>Published as part of <i>Chu, Kelin, Zhou, Lijun & Sun, Hongying, 2017, A new genus and new species of freshwater crab (Decapoda: Brachyura: Potamidae Ortmann, 1896) from Yunnan Province, China, pp. 241-253 in Zootaxa 4286 (2)</i> on pages 245-250, DOI: 10.11646/zootaxa.4286.2.7, <a href="http://zenodo.org/record/828451">http://zenodo.org/record/828451</a&gt

Planification des salles opératoires: résolution par la génération de colonne et la programmation dynamique

Dans cet article, nous nous intéressons au problème de planification des salles d'opératoires identiques. L'horaire d'ouverture et de fermeture est le même pour tous les salles. Nous présentons dans un premier temps le problème étudié dans sa globalité, à savoir le bloc opératoire. Nous donnons les caractéristiques de ce problème et sa modélisation sous forme d'un programme mathématique. Nous détaillons ensuite les approches de résolution. Nous avons opté ici pour deux méthodes : la génération de colonnes et la programmation dynamique. Les expérimentations seront effectuées à la fois sur des données générées aléatoirement suivant différentes lois statistiques, et sur des données réelles

A new genus and species of primary freshwater crab and a new species of Artopotamon Dai & Chen, 1985 (Crustacea, Brachyura, Potamidae) from western Yunnan, China

Chu, Kelin, Wang, Pengfei, Sun, Hongying (2018): A new genus and species of primary freshwater crab and a new species of Artopotamon Dai & Chen, 1985 (Crustacea, Brachyura, Potamidae) from western Yunnan, China. Zootaxa 4422 (1): 115-131, DOI: 10.11646/zootaxa.4422.1.

A planning and scheduling problem for an operating theatre using an open scheduling strategy

The objective of this paper is to design a weekly surgery schedule in an operating theatre where time blocks are reserved for surgeons rather than specialities. Both operating rooms and places in the recovery room are assumed to be multifunctional, and the objectives are to maximise the utilisation of the operating rooms, to minimise the overtime cost in the operating theatre, and to minimise the unexpected idle time between surgical cases. This weekly operating theatre planning and scheduling problem is solved in two phases. First, the planning problem is solved to give the date of surgery for each patient, allowing for the availability of operating rooms and surgeons. Then a daily scheduling problem is devised to determine the sequence of operations in each operating room in each day, taking into account the availability of recovery beds. The planning problem is described as a set-partitioning integer-programming model and is solved by a column-generation-based heuristic (CGBH) procedure. The daily scheduling problem, based on the results obtained in the planning phase, is treated as a two-stage hybrid flow-shop problem and solved by a hybrid genetic algorithm (HGA). Our results are compared with several actual surgery schedules in a Belgian university hospital, where time blocks have been assigned to either specific surgeons or specialities several months in advance. According to the comparison results, surgery schedules obtained by the proposed method have less idle time between surgical cases, much higher utilisation of operating rooms and produce less overtime

Solving a tactical operating room planning problem by a column-generation-based heuristic procedure with four criteria

In some hospitals, an “open scheduling” strategy is applied to solve the operating room planning problem; i.e., surgeons can choose any workday for his surgical cases, and the staffing of anesthetists and nurses is adjusted to maximize the efficiency of operating room utilization. In this paper, we aim at obtaining an efficient operating program for an operating theatre with several multifunctional operating rooms by using this “open scheduling” strategy. First, a mathematical model is constructed to assign surgical cases to operating rooms within one week. This model complies with the availability of operating rooms and surgeons, and its objective is not only to maximize utilization of operating rooms, but to minimize their overtime cost. Then a column-generation-based heuristic (CGBH) procedure is proposed, where four different criteria are compared with each other so as to find a solution with the best performance. In addition, the best approximate solution, obtained by this CGBH procedure after running all the criteria proposed, is compared with the lower bound obtained by an explicit column generation (CG) procedure, LP, to evaluate the distance between the approximate solution obtained and the optimum one. Although no criterion, according to the experimental results, is found superior to all other three in both robustness and quality of the solution obtained, it is found that the best solution obtained among those four criteria is often very close to LP, which means that the proposed algorithm can obtain a near optimal solution. In one word, the CGBH procedure proposed in this paper can obtain an efficient assignment of the surgical cases if the other resources (anesthesia and nursing staff, equipment, beds in the recovery room and etc.) are well organized

A memetic algorithm for Operating room scheduling

Operating theatre is always the most important and expensive sector of hospitals. Considering the recent environment pressure, this rector is surely to be significant to health-care institutions' managers when they regard cost reduction programs as a primary tool for managing the system's profitability. Our study aims to find out and efficient tool to minimize the total overtime cost of the operating theatre planning, especially the operating rooms (ORs) scheduling