LLukas22/scidocs huggingface dataset:
Discrepancy in clinical versus radiological parameters describing deformity due to brace treatment for moderate idiopathic scoliosis

BACKGROUND
The shape of the torso in patients with idiopathic scoliosis is considered to reflect the shape of the vertebral column, however the direct correlation between parameters describing clinical deformity and those characterizing radiological curvature was reported to be weak. It is not clear if the management proposed for scoliosis (physiotherapy, brace, surgery) affects equally the shape of the axial skeleton and the surface of the body. The aim of the study was to compare clinical deformity of (1) idiopathic scoliosis girls being under brace treatment for radiological curves of 25 to 40 degrees and (2) non treated scoliotic girls matched for age and Cobb angle.


METHODS
Cross-sectional study of 24 girls wearing the brace versus 26 girls without brace treatment, matched for age and Cobb angle.


HYPOTHESIS
Patients wearing the brace for more than 6 months, when comparing to patients without brace, may present different external morphology of the trunk, in spite of having similar Cobb angle. Material.


INCLUSION CRITERIA
girls, idiopathic scoliosis, growing age (10-16 years), Cobb angle minimum 25 degrees , maximum 40 degrees . The braced group consisted of girls wearing a TLSO brace (Cheneau) for more than 6 months with minimum of 16 hours per day. The non-braced group consisted of girls first seen for their spinal deformity, previously not treated. The groups presented similar curve pattern. Methods. Scoliometer exam: angle of trunk rotation at three levels of the spine: upper thoracic, main thoracic, lumbar or thoracolumbar. The maximal angle was noted at each level and the sum of three levels was calculated. Posterior trunk symmetry index (POTSI) and Hump Sum were measured using surface topography.


RESULTS
Cobb angle was 34.9 degrees +/- 4.8 degrees in braced and 32.7 degrees +/- 4.9 degrees in un-braced patients (difference not significant). The age was 14.1 +/- 1.6 years in braced patients and 13.1 +/- 1.9 years in un-braced group (p = 0.046). The value of angle of trunk rotation in the main curvature was 8.4 degrees +/- 2.7 degrees in braced and 11.4 degrees +/- 2.7 degrees in un-braced patients (difference extremely significant, p = 0.0003). The value of the sum of angles of trunk rotation at three levels of the trunk was 12.8 degrees +/- 4.6 degrees in braced and 16.5 degrees +/- 3.8 degrees in un-braced patients (difference very significant, p = 0.0038). The POTSI did not differ significantly between the groups (p = 0.78), the Hump Sum values were not quite different (p = 0.07).


CONCLUSION
(1) Adolescent girls wearing the brace for idiopathic scoliosis of 25 to 40 degrees of Cobb angle, reveal smaller clinical rotational deformity of their back than non-treated girls having similar radiological deformity. (2) Evaluation of the results of treatment for idiopathic scoliosis should consider parameters describing both clinical and radiological deformity.
Automated segmentation and analysis of normal and osteoarthritic knee menisci from magnetic resonance images--data from the Osteoarthritis Initiative.

OBJECTIVE
To validate an automatic scheme for the segmentation and quantitative analysis of the medial meniscus (MM) and lateral meniscus (LM) in magnetic resonance (MR) images of the knee.


METHOD
We analysed sagittal water-excited double-echo steady-state MR images of the knee from a subset of the Osteoarthritis Initiative (OAI) cohort. The MM and LM were automatically segmented in the MR images based on a deformable model approach. Quantitative parameters including volume, subluxation and tibial-coverage were automatically calculated for comparison (Wilcoxon tests) between knees with variable radiographic osteoarthritis (rOA), medial and lateral joint space narrowing (mJSN, lJSN) and pain. Automatic segmentations and estimated parameters were evaluated for accuracy using manual delineations of the menisci in 88 pathological knee MR examinations at baseline and 12 months time-points.


RESULTS
The median (95% confidence-interval (CI)) Dice similarity index (DSI) (2 ∗|Auto ∩ Manual|/(|Auto|+|Manual|)∗ 100) between manual and automated segmentations for the MM and LM volumes were 78.3% (75.0-78.7), 83.9% (82.1-83.9) at baseline and 75.3% (72.8-76.9), 83.0% (81.6-83.5) at 12 months. Pearson coefficients between automatic and manual segmentation parameters ranged from r = 0.70 to r = 0.92. MM in rOA/mJSN knees had significantly greater subluxation and smaller tibial-coverage than no-rOA/no-mJSN knees. LM in rOA knees had significantly greater volumes and tibial-coverage than no-rOA knees.


CONCLUSION
Our automated method successfully segmented the menisci in normal and osteoarthritic knee MR images and detected meaningful morphological differences with respect to rOA and joint space narrowing (JSN). Our approach will facilitate analyses of the menisci in prospective MR cohorts such as the OAI for investigations into pathophysiological changes occurring in early osteoarthritis (OA) development.
Determinants of fertilizer and manure use for maize production in Kiambu District, Kenya

Farms in Kiambu District are very small owing to high population pressure and need to be intensively farmed to provide enough food for consumption and sale. Since soil nitrogen levels are low, the use of inorganic fertilizers and manure needs to be increased to improve land productivity. This study identified the socioeconomic factors influencing the use of inorganic fertilizers and manure for maize production in Kiambu District. A multistage sampling procedure was used to select divisions and farmers to be included in the study. Three divisions were randomly selected, from which a sample of 97 farmers was obtained. Data were collected at the farm level using a structured questionnaire. Soil and manure samples were taken from sample farms for laboratory analysis. The soil analysis showed that soils in Kiambu District have a high organic carbon content (3-4%), which reflects high levels of applied organic matter, most likely coupled with low rates of mineralization. Soils are low in nitrogen (N), indicating that more N needs to be added. Phosphorus (P) levels are not severely limiting, which might reflect a build-up of previously applied P. The logistic regression showed that extension and off-farm income were significant factors influencing the adoption of manure. Age of household head, extension, membership in an organization, and off-farm income significantly influenced the use of inorganic fertilizer. The use of both inorganic fertilizer and manure was significantly influenced by extension, membership in an organization, household size, hired labor for manure application, livestock ownership, and off-farm income. Extension, the most significant factor affecting the use of manure and fertilizer, should promote adoption by providing advice on improved on-farm manure management and fertilizer recommendations, particularly in terms of crop suitability and timing and method of application. Also, the extension service should advise fertilizer dealers to supply the packages required by farmers. To further aid adoption, capital (credit) constraints faced by farmers need to be relieved. Improved market information will assist farmers in securing the best prices for their outputs and inputs. ISBN: 970-648-070-6 AGROVOC descriptors: Zea mays; maize; Plant production; Production factors; Fertilizers; Green manures; Fertilizer application; Innovation adoption; Input output analysis; Kenya AGRIS category codes: E14 Development Economics and Policies F04 Fertilizing Dewey decimal classification: 338.16 Additional keywords: CIMMYT
Prediction of Cell Penetrating Peptides by Support Vector Machines

Cell penetrating peptides (CPPs) are those peptides that can transverse cell membranes to enter cells. Once inside the cell, different CPPs can localize to different cellular components and perform different roles. Some generate pore-forming complexes resulting in the destruction of cells while others localize to various organelles. Use of machine learning methods to predict potential new CPPs will enable more rapid screening for applications such as drug delivery. We have investigated the influence of the composition of training datasets on the ability to classify peptides as cell penetrating using support vector machines (SVMs). We identified 111 known CPPs and 34 known non-penetrating peptides from the literature and commercial vendors and used several approaches to build training data sets for the classifiers. Features were calculated from the datasets using a set of basic biochemical properties combined with features from the literature determined to be relevant in the prediction of CPPs. Our results using different training datasets confirm the importance of a balanced training set with approximately equal number of positive and negative examples. The SVM based classifiers have greater classification accuracy than previously reported methods for the prediction of CPPs, and because they use primary biochemical properties of the peptides as features, these classifiers provide insight into the properties needed for cell-penetration. To confirm our SVM classifications, a subset of peptides classified as either penetrating or non-penetrating was selected for synthesis and experimental validation. Of the synthesized peptides predicted to be CPPs, 100% of these peptides were shown to be penetrating.
Impact of Programming Features on Code Readability

Readability is one important quality attributes for software source codes. Readability has also significant relation or impact with other quality attributes such as: reusability, maintainability, reliability, complexity, and portability metrics. This research develops a novel approach called Impact of Programming Features on Code Readability (IPFCR), to examine the influence of various programming features and the effect of these features on code readability. A code Readability Tool (CRT) is developed to evaluate the IPFCR readability features or attributes. In order to assess the level if impact that each one of the 25 proposed readability features may have, positively or negatively on the overall code readability, a survey was distributed to a random number of expert programmers. These experts evaluated the effect of each feature on code readability, based on their knowledge or experience. Expert programmers have evaluated readability features to be ordered then classified into positive and negative factors based on their impact on code readability or understanding. The survey responses were analyzed using SPSS statistical tool. Most of proposed code features showed to have significantly positive impact on enhancing readability including: meaningful names, consistency, and comments. On the other hand, fewer features such as arithmetic formulas, nested loops, and recursive functions showed to have a negative impact. Finally, few features showed to have neutral impact on readability.
Hydrolysis of orange peel with pectinase and cellulase enzymes

Hydrolysis of polysaccharides in comminuted orange peel by commercial cellulase and pectinase enzymes has been investigated. High levels of conversion to monomeric sugars were observed after treatment with pectinase enzyme, but cellulase enzyme achieved only limited solubilization. The combination of cellulase and pectinase enzymes appears to be a most efficient system for enzymatic hydrolysis of polysaccharides in orange peel.
Temporal filtering for depth maps generated by Kinect depth camera

We propose a method of filtering depth maps provided by Kinect depth camera. Filter uses output of the conventional Kinect camera along with the depth sensor to improve the temporal stability of the depth map and fill occlusion areas. To filter input depth map, the algorithm uses the information about motion and color of objects from the video. The proposed method can be applied as a preprocessing stage before using Kinect output data.
Augustinian Christian Philosophy

How does Christianity bear on philosophy? Is there such a thing as Christian philosophy, or are there only Christians who are also philoso phers? How should Christianity and philosophy be related? Should they be related? In "Advice to Christian Philosophers" I said that Christian philosophers should display more autonomy: they have their own fish to fry, their own projects to pursue, (or their own axes to grind, as some might prefer to put it). Here I want to say more about what these projects (or fish, or axes) are like. And the right way to think about these matters, so it seems to me, is broadly Augustinian. Accordingly, I want to propose a program matic sketch (a very programmatic sketch) of a conception of Christian philosophy that grows out of some central Augustinian emphases. I don't claim, however, that Augustine in fact thought of Christian philosophy the way I shall suggest. The primary focus of my paper is not historical (that would in any event be beyond my competence); what I want to do is make a suggestion as to how we should think about Christian philosophy now; but this way of thinking of the matter grows out of Augustinian roots.1 It's worth noting, furthermore, that what is at issue is not just a way of thinking about Christianity and philosophy, but about Christianity and scholarship more generally. There are at least four elements in Augustinian Christian philosophy. The first two of these are widely recognized and relatively uncontroversial: I shall therefore be brief about them. The remaining two, however, require more by way of explanation, illustration and defense.
Effect of Xiaoyu Zhixue Tablet on the expression of platelet membrane glycoprotein I b/IX/V complex in patients with chronic renal failure.

OBJECTIVE
To investigate the effect of Xiaoyu Zhixue Tablet (XYZXT) on the expression of platelet membrane glycoprotein (GP) Ib/IX/V complex and GP I b alpha in patients with chronic renal failure (CRF) in early metaphase.


METHODS
Fifty-one patients with CRF in early metaphase (treated group) were treated with XYZXT, 3 months as the course of treatment for 2 courses. The previous therapies remained unchanged. Flow cytometry was used to assess the expression of platelet GP Ib/IX/V complex and GP Ib alpha in patients with CRF, and turbidity method was used to determine the platelet maximum aggregation rate (MAR), meanwhile the renal function was measured. The final data were compared with those before the treatment, and with those in the normal control group (31 healthy subjects).


RESULTS
Compared with the normal control group, expressions of GP I b/IX/V complex and GP I b alpha, and platelet MAR in CRF patients were significantly lower (P=0.007, P=0.001, P=0.009) before the treatment; after the treatment with XYZXT, the above indexes in CRF patients were remarkably increased (P=0.033, P=0.026, P=0.045), but still lower than those in the normal control group, however, it was not statistically significant.


CONCLUSION
(1) The expression of GP I b/IX/V complex in CRF patients of early metaphase was decreased, which lead to platelet aggregation dysfunction. This might be one of the reasons for the hemorrhagic trend in CRF. (2) XYZXT was able to upgrade expressions of GP I b/IX/V complex and GP I b alpha in CRF patients, improve platelet function and down-regulate platelet activation in patients with CRF.
Thinking may be more than computing

The uncomputable parts of thinking (if there are any) can be studied in much the same spirit that Turing (1950) suggested for the study of its computable parts. We can develop precise accounts of cognitive processes that, although they involve more than computing, can still be modelled on the machines we call ‘computers’. In this paper, I want to suggest some ways that this might be done, using ideas from the mathematical theory of uncomputability (or Recursion Theory). And I want to suggest some uses to which the resulting models might be put. (The reader more interested in the models and their uses than the mathematics and its theorems, might want to skim or skip the mathematical parts.)
Randomized controlled trial of skin-to-skin contact from birth versus conventional incubator for physiological stabilization in 1200- to 2199-gram newborns.

AIM
Conventional care of prematurely born infants involves extended maternal-infant separation and incubator care. Recent research has shown that separation causes adverse effects. Maternal-infant skin-to-skin contact (SSC) provides an alternative habitat to the incubator, with proven benefits for stable prematures; this has not been established for unstable or newborn low-birthweight infants. SSC from birth was therefore compared to incubator care for infants between 1200 and 2199 g at birth.


METHODS
This was a prospective, unblinded, randomized controlled clinical trial; potential subjects were identified before delivery and randomized by computerized minimization technique at 5 min if eligible. Standardized care and observations were maintained for 6 h. Stability was measured in terms of a set of pre-determined physiological parameters, and a composite cardio-respiratory stabilization score (SCRIP).


RESULTS
34 infants were analysed in comparable groups: 3/18 SSC compared to 12/13 incubator babies exceeded the pre-determined parameters (p < 0.001). Stabilization scores were 77.11 for SSC versus 74.23 for incubator (maximum 78), mean difference 2.88 (95% CI: 0.3-5.46, p = 0.031). All 18 SSC subjects were stable in the sixth hour, compared to 6/13 incubator infants. Eight out of 13 incubator subjects experienced hypothermia.


CONCLUSION
Newborn care provided by skin-to-skin contact on the mother's chest results in better physiological outcomes and stability than the same care provided in closed servo-controlled incubators. The cardio-respiratory instability seen in separated infants in the first 6 h is consistent with mammalian "protest-despair" biology, and with "hyper-arousal and dissociation" response patterns described in human infants: newborns should not be separated from their mothers.
Non-nutritive sucking and facilitated tucking relieve preterm infant pain during heel-stick procedures: a prospective, randomised controlled crossover trial.

BACKGROUND
Preterm infants' repeated exposure to painful procedures may contribute to negative consequences. Thus, improving preterm infants' neurodevelopmental outcomes requires prioritising their pain management.


OBJECTIVES
To compare the effectiveness of two non-pharmacological pain-relief strategies (non-nutritive sucking and facilitated tucking) with routine care on preterm infants' pain, behavioural, and physiological responses before, during, and after heel-stick procedures.


DESIGN
Prospective, randomised controlled crossover trial.


SETTING
Level III Neonatal Intensive Care Unit in Taipei.


METHOD
Thirty-four preterm infants (gestational age 29-37 weeks) needing three procedural heel sticks were recruited by convenience sampling and randomly assigned to a sequence of three treatments (two pain-relief interventions and the control condition): (1) routine care, non-nutritive sucking, facilitated tucking, (2) non-nutritive sucking, facilitated tucking, routine care, and (3) facilitated tucking, routine care, non-nutritive sucking. Each treatment condition was performed on a different day to avoid any carry-over effect. Pain was measured by the Premature Infant Pain Profile (PIPP), infant behaviour by a behavioural coding scheme, and physiological signals by electrocardiogram monitors. All data were collected 3 min without stimuli (baseline), during heel-stick procedures, and recovery.


RESULTS
Infants receiving non-nutritive sucking and facilitated tucking had significantly lower mean (standard deviation) pain scores during heel-stick procedures (6.39 [3.35] and 7.15 [3.88], respectively) than those receiving routine care (9.52 [4.95]). Infants receiving non-nutritive sucking and facilitated tucking had significantly lower odds ratios (0.39, p=0.011 and 0.34, p=0.005, respectively) for pain (PIPP score≥6) than infants receiving routine care after adjusting for time, baseline pain scores, and infants' characteristics. Similarly, infants receiving non-nutritive sucking and facilitated tucking had significantly lower odds ratios (0.23, p<0.001 and 0.28, p=0.03, respectively) for moderate-to-severe pain (PIPP score≥12) than infants receiving routine care. Infants receiving facilitated tucking had lower frequency ratios for stress-related behaviours, abnormal heart rates, and decreased oxygen saturation than infants receiving routine care.


CONCLUSIONS
Both non-nutritive sucking and facilitated tucking effectively reduced pain scores more than routine care during heel-stick procedures. Non-nutritive sucking reduced PIPP pain scores more effectively than facilitated tucking. However, facilitated tucking showed broader effects not only on relieving pain, but also on enhancing infants' physiological and behavioural stability during heel-stick procedures.
Approximation Algorithms for Multiple Sequence Alignment Under a Fixed Evolutionary Tree

We consider the problem of multiple sequence alignment under a xed evolu tionary tree given a tree whose leaves are labeled by sequences nd ancestral sequences to label its internal nodes so as to minimize the total length of the tree where the length of an edge is the edit distance between the sequences labeling its endpoints We present a new polynomial time approximation algorithm for this problem and analyze its performance on regular d ary trees with d a constant On such a tree the algorithm nds a solution within a factor d d of the minimum in O kT d n k n time where k is the number of leaves in the tree n is the length of the longest sequence labeling a leaf and T d n is the time to compute a Steiner point for d sequences of length at most n A Steiner point for a set S of sequences is a sequence P that minimizes the sum of the edit distances from P to each sequence in S The time T d n is O d n given O ds time preprocessing for an alphabet of size s The approximation algorithm is conceptually simple and easy to implement and actually applies to any metric space in which a Steiner point for any xed sized set can be computed in polynomial time We also introduce a new problem bottleneck tree alignment in which the objective is to label the internal nodes of the tree so as to minimize the length of the longest edge We describe an exponential time exact algorithm for the case of unit cost edit operations and show there is a simple linear time approximation algorithm for the general case that nds a solution within a factor O log k of the minimum