Slice and Dice: A Physicalization Workflow for Anatomical Edutainment

During the last decades, anatomy has become an interesting topic in education---even for laymen or schoolchildren. As medical imaging techniques become increasingly sophisticated, virtual anatomical education applications have emerged. Still, anatomical models are often preferred, as they facilitate 3D localization of anatomical structures. Recently, data physicalizations (i.e., physical visualizations) have proven to be effective and engaging---sometimes, even more than their virtual counterparts. So far, medical data physicalizations involve mainly 3D printing, which is still expensive and cumbersome. We investigate alternative forms of physicalizations, which use readily available technologies (home printers) and inexpensive materials (paper or semi-transparent films) to generate crafts for anatomical edutainment. To the best of our knowledge, this is the first computer-generated crafting approach within an anatomical edutainment context. Our approach follows a cost-effective, simple, and easy-to-employ workflow, resulting in assemblable data sculptures (i.e., semi-transparent sliceforms). It primarily supports volumetric data (such as CT or MRI), but mesh data can also be imported. An octree slices the imported volume and an optimization step simplifies the slice configuration, proposing the optimal order for easy assembly. A packing algorithm places the resulting slices with their labels, annotations, and assembly instructions on a paper or transparent film of user-selected size, to be printed, assembled into a sliceform, and explored. We conducted two user studies to assess our approach, demonstrating that it is an initial positive step towards the successful creation of interactive and engaging anatomical physicalizations

Untangling Circular Drawings: Algorithms and Complexity

We consider the problem of untangling a given (non-planar) straight-line circular drawing $\delta_G$ of an outerplanar graph $G=(V, E)$ into a planar straight-line circular drawing by shifting a minimum number of vertices to a new position on the circle. For an outerplanar graph $G$, it is clear that such a crossing-free circular drawing always exists and we define the circular shifting number shift$(\delta_G)$ as the minimum number of vertices that are required to be shifted in order to resolve all crossings of $\delta_G$. We show that the problem Circular Untangling, asking whether shift$(\delta_G) \le K$ for a given integer $K$, is NP-complete. For $n$-vertex outerplanar graphs, we obtain a tight upper bound of shift$(\delta_G) \le n - \lfloor\sqrt{n-2}\rfloor -2$. Based on these results we study Circular Untangling for almost-planar circular drawings, in which a single edge is involved in all the crossings. In this case, we provide a tight upper bound shift$(\delta_G) \le \lfloor \frac{n}{2} \rfloor-1$ and present a constructive polynomial-time algorithm to compute the circular shifting number of almost-planar drawings.Comment: 20 pages, 10 figures, extended version of ISAAC 2021 pape

Conserved charged amino acid residues in the extracellular region of sodium/iodide symporter are critical for iodide transport activity

<p>Abstract</p> <p>Background</p> <p>Sodium/iodide symporter (NIS) mediates the active transport and accumulation of iodide from the blood into the thyroid gland. His-226 located in the extracellular region of NIS has been demonstrated to be critical for iodide transport in our previous study. The conserved charged amino acid residues in the extracellular region of NIS were therefore characterized in this study.</p> <p>Methods</p> <p>Fourteen charged residues (Arg-9, Glu-79, Arg-82, Lys-86, Asp-163, His-226, Arg-228, Asp-233, Asp-237, Arg-239, Arg-241, Asp-311, Asp-322, and Asp-331) were replaced by alanine. Iodide uptake abilities of mutants were evaluated by steady-state and kinetic analysis. The three-dimensional comparative protein structure of NIS was further modeled using sodium/glucose transporter as the reference protein.</p> <p>Results</p> <p>All the NIS mutants were expressed normally in the cells and targeted correctly to the plasma membrane. However, these mutants, except R9A, displayed severe defects on the iodide uptake. Further kinetic analysis revealed that mutations at conserved positively charged amino acid residues in the extracellular region of NIS led to decrease NIS-mediated iodide uptake activity by reducing the maximal rate of iodide transport, while mutations at conserved negatively charged residues led to decrease iodide transport by increasing dissociation between NIS mutants and iodide.</p> <p>Conclusions</p> <p>This is the first report characterizing thoroughly the functional significance of conserved charged amino acid residues in the extracellular region of NIS. Our data suggested that conserved charged amino acid residues, except Arg-9, in the extracellular region of NIS were critical for iodide transport.</p

Regulation of clpQ+Y+ (hslV+U+) Gene Expression in Escherichia coli

The Escherichia coli ClpYQ (HslUV) complex is an ATP-dependent protease, and the clpQ+Y+ (hslV+U+) operon encodes two heat shock proteins, ClpQ and ClpY, respectively. The transcriptional (op) or translational (pr) clpQ+::lacZ fusion gene was constructed, with the clpQ+Y+ promoter fused to a lacZ reporter gene. The clpQ+::lacZ (op or pr) fusion gene was each crossed into lambda phage. The λclpQ+::lacZ+ (op), a transcriptional fusion gene, was used to form lysogens in the wild-type, rpoH or/and rpoS mutants. Upon shifting the temperature up from 30 °C to 42 °C, the wild-type λclpQ+::lacZ+ (op) demonstrates an increased β-galactosidase (βGal) activity. However, the βGal activity of clpQ+::lacZ+ (op) was decreased in the rpoH and rpoH rpoS mutants but not in the rpoS mutant. The levels of clpQ+::lacZ+ mRNA transcripts correlated well to their βGal activity. Similarly, the expression of the clpQ+::lacZ+ gene fusion was nearly identical to the clpQ+Y+ transcript under the in vivo condition. The clpQm1::lacZ+, containing a point mutation in the -10 promoter region for RpoH binding, showed decreased βGal activity, independent of activation by RpoH. We conclude that RpoH itself regulates clpQ+Y+ gene expression. In addition, the clpQ+Y+ message carries a conserved 71 bp at the 5’ untranslated region (5’UTR) that is predicted to form the stem-loop structure by analysis of its RNA secondary structure. The clpQm2Δ40::lacZ+, with a 40 bp deletion in the 5’UTR, showed a decreased βGal activity. In addition, from our results, it is suggested that this stem-loop structure is necessary for the stability of the clpQ+Y+ message

Urinary acrolein protein conjugates-tocreatinine ratio is positively associated with diabetic peripheral neuropathy in patients with type 2 diabetes mellitus

Acrolein, an unsaturated aldehyde, plays a pathological role in neurodegenerative diseases. However, less is known about its effects on peripheral neuropathy. The aim of this study was to investigate the association of acrolein and diabetic peripheral neuropathy in patients with type 2 diabetes. We recruited 148 ambulatory patients with type 2 diabetes. Each participant underwent an assessment of the Michigan Neuropathy Screening Instrument Physical Examination. Diabetic peripheral neuropathy was defined as Michigan Neuropathy Screening Instrument Physical Examination score ≥ 2.5. Serum levels and urinary levels of acrolein protein conjugates were measured. Urinary acrolein protein conjugates-to-creatinine ratios were determined. Patients with diabetic peripheral neuropathy had significantly higher urinary acrolein protein conjugates-to-creatinine ratios than those without diabetic peripheral neuropathy (7.91, 95% CI: 5.96–10.50 vs 5.31, 95% CI: 4.21–6.68, P = 0.029). Logarithmic transformation of urinary acrolein protein conjugates-to-creatinine ratios was positively associated with diabetic peripheral neuropathy in univariate logistic analysis, and the association remained significant in multivariate analysis (OR = 2.45, 95% CI: 1.12–5.34, P = 0.025). In conclusion, urinary acrolein protein conjugates-to-creatinine ratio may act as a new biomarker for diabetic peripheral neuropathy in type 2 diabetes. The involvement of acrolein in the pathogenesis of diabetic peripheral neuropathy warrants further investigation

Extending the Pre-Training of BLOOM for Improved Support of Traditional Chinese: Models, Methods and Results

In this paper we present the multilingual language model BLOOM-zh that features enhanced support for Traditional Chinese. BLOOM-zh has its origins in the open-source BLOOM models presented by BigScience in 2022. Starting from released models, we extended the pre-training of BLOOM by additional 7.4 billion tokens in Traditional Chinese and English covering a variety of domains such as news articles, books, encyclopedias, educational materials as well as spoken language. In order to show the properties of BLOOM-zh, both existing and newly created benchmark scenarios are used for evaluating the performance. BLOOM-zh outperforms its predecessor on most Traditional Chinese benchmarks while maintaining its English capability. We release all our models to the research community