Public Participation’ Development in Trenggalek Regency’ Legal Drafting Through Support Budgeting

This paper focuses on explaining the idea of developing public participation in Trenggalek Regency’ legal drafting through support budgeting. The results of the study is based on the budgeting support’ model for the participation of the public through the Region Revenues and Expenditures Budget (APBD) which was further analyzed through the theory of participation and the theory of law enforcement. The results show that support budgeting is still centered on the activities of regulators and has not yet created a budgeting system that is aimed specifically towards the development of public’ participation. There has not been a good application yet of the theory of participation and the theory of law enforcement in the preparation of APBD. This, however, is attributed to the fact that the budget system has not fully supported the development of Public participation in the regional regulations’ drafting. This problem can be solved with a good and same understanding about the meaningful Public participation in the regional regulations’ drafting among the regulators

Skin Segmentation and Skull Segmentation for Medical Imaging

In this paper aims we present tools for medical imaging applications to do skin and skull segmentation in a short time. The desired output for skin segmentation is a 3D visualization of the facial skin without any cavities or holes inside the head, while skull segmentation aims to create a 3D visualization of the skull bones. The algorithm used for skin segmentation is thresholding the image, extracting the largest connected component, and holefilling to fill the unnecessary holes. As for the skull segmentation, the process is done by removing the spines which is connected to the skull, and then extracting the largest connected component. Afterwards, mesh generation is done to produce the 3D objects from the processed images. This mesh generation process is done using the marching cubes algorithm. The testing results show that the skin and skull segmentation process will work well when there are no other objects that are connected to the skin or the skull. Skin segmentation process takes a significant amount of time, primarily caused by the holefilling process

Variasi Kuat Kokoh Tanah Lempung Ekspansif Akibat Perubahan Musim

Tanah lempung ekspansif yang tidak diperhitungkan dengan baik dapat mengakibatkan kerusakan pada struktur bangunan. Wetting dan drying, merupakan sebuah metode yang digunakan untuk mengetahui kondisi tanah pada saat musim hujan dan kemarau. Proses wetting dilakukan dengan cara tanah dibasahi untuk mencari beratnya sedangkan drying dilakukan dengan cara tanah dikeringkan pada ruangan tertutup untuk mencari beratnya. Tujuan dari penelitian ini adalah mengetahui pengaruh indeks plastisitas dan persentase fine aggregate terhadap Perubahan kuat kokoh akibat wetting dan drying. Karakteristik tanah pada kondisi mula-mula dari lima lokasi di Surabaya Barat didapatkan dari pengujian di laboratorium UK Petra. Pada saat proses wetting, tanah dibasahi sampai berat tanah yang diinginkan, sedangkan pada proses drying tanah dibiarkan di ruangan sampai mencapai berat tanah yang diinginkan. Hasil dari penelitian ini menunjukkan bahwa nilai indeks plastisitas yang semakin tinggi mengakibatkan range kuat kokoh yang kecil, dan persentase fine aggregate yang semakin tinggi mengakibatkan range kuat kokoh yang besar

Conformational changes of calmodulin upon Ca2+ binding studied with a microfluidic mixer

A microfluidic mixer is applied to study the kinetics of calmodulin conformational changes upon Ca2+ binding. The device facilitates rapid, uniform mixing by decoupling hydrodynamic focusing from diffusive mixing and accesses time scales of tens of microseconds. The mixer is used in conjunction with multiphoton microscopy to examine the fast Ca2+-induced transitions of acrylodan-labeled calmodulin. We find that the kinetic rates of the conformational changes in two homologous globular domains differ by more than an order of magnitude. The characteristic time constants are ≈490 μs for the transitions in the C-terminal domain and ≈20 ms for those in the N-terminal domain of the protein. We discuss possible mechanisms for the two distinct events and the biological role of the stable intermediate, half-saturated calmodulin

Estimation of interdomain flexibility of N-terminus of factor H using residual dipolar couplings

Characterization of segmental flexibility is needed to understand the biological mechanisms of the very large category of functionally diverse proteins, exemplified by the regulators of complement activation, that consist of numerous compact modules or domains linked by short, potentially flexible, sequences of amino acid residues. The use of NMR-derived residual dipolar couplings (RDCs), in magnetically aligned media, to evaluate interdomain motion is established but only for two-domain proteins. We focused on the three N-terminal domains (called CCPs or SCRs) of the important complement regulator, human factor H (i.e. FH1-3). These domains cooperate to facilitate cleavage of the key complement activation-specific protein fragment, C3b, forming iC3b that no longer participates in the complement cascade. We refined a three-dimensional solution structure of recombinant FH1-3 based on nuclear Overhauser effects and RDCs. We then employed a rudimentary series of RDC datasets, collected in media containing magnetically aligned bicelles (disk-like particles formed from phospholipids) under three different conditions, to estimate interdomain motions. This circumvents a requirement of previous approaches for technically difficult collection of five independent RDC datasets. More than 80% of conformers of this predominantly extended three-domain molecule exhibit flexions of < 40 °. Such segmental flexibility (together with the local dynamics of the hypervariable loop within domain 3), could facilitate recognition of C3b via initial anchoring and eventual reorganization of modules to the conformation captured in the previously solved crystal structure of a C3b:FH1-4 complex

A unifying probabilistic framework for analyzing residual dipolar couplings

Residual dipolar couplings provide complementary information to the nuclear Overhauser effect measurements that are traditionally used in biomolecular structure determination by NMR. In a de novo structure determination, however, lack of knowledge about the degree and orientation of molecular alignment complicates the analysis of dipolar coupling data. We present a probabilistic framework for analyzing residual dipolar couplings and demonstrate that it is possible to estimate the atomic coordinates, the complete molecular alignment tensor, and the error of the couplings simultaneously. As a by-product, we also obtain estimates of the uncertainty in the coordinates and the alignment tensor. We show that our approach encompasses existing methods for determining the alignment tensor as special cases, including least squares estimation, histogram fitting, and elimination of an explicit alignment tensor in the restraint energy

CS23D: a web server for rapid protein structure generation using NMR chemical shifts and sequence data

CS23D (chemical shift to 3D structure) is a web server for rapidly generating accurate 3D protein structures using only assigned nuclear magnetic resonance (NMR) chemical shifts and sequence data as input. Unlike conventional NMR methods, CS23D requires no NOE and/or J-coupling data to perform its calculations. CS23D accepts chemical shift files in either SHIFTY or BMRB formats, and produces a set of PDB coordinates for the protein in about 10–15 min. CS23D uses a pipeline of several preexisting programs or servers to calculate the actual protein structure. Depending on the sequence similarity (or lack thereof) CS23D uses either (i) maximal subfragment assembly (a form of homology modeling), (ii) chemical shift threading or (iii) shift-aided de novo structure prediction (via Rosetta) followed by chemical shift refinement to generate and/or refine protein coordinates. Tests conducted on more than 100 proteins from the BioMagResBank indicate that CS23D converges (i.e. finds a solution) for >95% of protein queries. These chemical shift generated structures were found to be within 0.2–2.8 Å RMSD of the NMR structure generated using conventional NOE-base NMR methods or conventional X-ray methods. The performance of CS23D is dependent on the completeness of the chemical shift assignments and the similarity of the query protein to known 3D folds. CS23D is accessible at http://www.cs23d.ca

Solution structure of a repeated unit of the ABA-1 nematode polyprotein allergen of ascaris reveals a novel fold and two discrete lipid-binding sites

Parasitic nematode worms cause serious health problems in humans and other animals. They can induce allergic-type immune responses, which can be harmful but may at the same time protect against the infections. Allergens are proteins that trigger allergic reactions and these parasites produce a type that is confined to nematodes, the nematode polyprotein allergens (NPAs). These are synthesized as large precursor proteins comprising repeating units of similar amino acid sequence that are subsequently cleaved into multiple copies of the allergen protein. NPAs bind small lipids such as fatty acids and retinol (Vitamin A) and probably transport these sensitive and insoluble compounds between the tissues of the worms. Nematodes cannot synthesize these lipids, so NPAs may also be crucial for extracting nutrients from their hosts. They may also be involved in altering immune responses by controlling the lipids by which the immune and inflammatory cells communicate. We describe the molecular structure of one unit of an NPA, the well-known ABA-1 allergen of Ascaris and find its structure to be of a type not previously found for lipid-binding proteins, and we describe the unusual sites where lipids bind within this structur