Novel Method for Restitution of a Torqued and Entrapped Kinked 7F Catheter in the Ascending Aorta

Knotting and kinking of diagnostic coronary artery catheters are potentially catastrophic complications though their occurrence is uncommon. However, abrupt kinking of 7F guide catheters in the ascending aorta becomes a quirky puzzle. This case emphasizes the importance of avoiding kinking and provides recommendations for catheter retrieval in the unlikely event of this complication. To the best of our knowledge, the technique used in our case has not been described before.

Knot Formation on DNA Pushed Inside Chiral Nanochannels

We performed coarse-grained molecular dynamics simulations of DNA polymers pushed inside infinite open chiral and achiral channels. We investigated the behavior of the polymer metrics in terms of span, monomer distributions and changes of topological state of the polymer in the channels. We also compared the regime of pushing a polymer inside the infinite channel to the case of polymer compression in finite channels of knot factories investigated in earlier works. We observed that the compression in the open channels affects the polymer metrics to different extents in chiral and achiral channels. We also observed that the chiral channels give rise to the formation of equichiral knots with the same handedness as the handedness of the chiral channels.

Knotwood and Branchwood Polyphenolic Extractives of Silver Fir, Spruce and Douglas Fir and Their Antioxidant, Antifungal and Antibacterial Properties

The extractive contents of three softwood species largely used in the wood industry, namely Abies alba (Silver fir), Picea abies (spruce) and Pseudotsuga menziesii (Douglas fir), have been determined quantitatively for knots and at different points chosen along their branches, before analysis using high-performance liquid chromatography coupled with Mass Spectrometry (HPLC-MS). The results indicated that branchwood samples located in close proximity to the stem present high contents of extractives similar to those recorded for the knots. HPLC analysis showed quite similar chemical compositions, indicating that first cm of the branches could be considered as an additional source of knotwood. The antibacterial, antifungal and antioxidant activities of knot's extractives have been investigated with the dual objective of better understanding the role of high levels of secondary metabolites present in the knot and evaluating their potential for biorefinery applications. The antioxidant activity study showed that crude extracts of Douglas fir knotwood presented higher radical scavenging activity levels than the extracts of Silver fir and spruce, which presented more or less the same activities. Silver fir and spruce knotwood extracts presented higher antibacterial activity levels than the Douglas fir knotwood extracts did, while Douglas fir knotwood extracts presented more fungal growth inhibition than the spruce and fir knotwood extracts did. The structure-activity relationships indicate that radical scavenging and antifungal activities are associated with a higher relative quantity of flavonoids in the crude extracts, while higher relative quantities of lignans are associated with antibacterial activity.

Association of placental and umbilical cord characteristics with cerebral palsy: national cohort study

OBJECTIVES

Cerebral palsy (CP) is a group of movement disorders usually diagnosed in childhood. A substantial proportion are thought to be caused by antenatal events. Abnormalities of the umbilical cord and placenta are associated with an increased risk of adverse neonatal outcomes, but it is unclear whether these conditions also carry an increased risk of CP. We aimed to determine whether abnormalities of the umbilical cord or placenta are associated with CP and assess if these associations differ by sex of the child or gestational age at birth.

METHODS

We performed a national cohort study by linking data from The Medical Birth Registry of Norway with other national registries. All liveborn singletons born between 1999 and 2017 (n = 1 087 486) were included and followed up until the end of 2019. Diagnoses of CP were provided by the Norwegian National Insurance Scheme and the Norwegian Patient Register. We used generalized estimating equations and multilevel log binomial regression to calculate relative risks (RR), adjusted for year of birth, and stratified analyses were carried out based on sex and gestational age at birth. Exposures were abnormal umbilical cord (velamentous or marginal insertion, single umbilical artery (SUA), knots and entanglement), and placental abnormalities (retained placenta, placental abruption and previa).

RESULTS

A total of 2443 cases with CP (59.8% males) were identified. Velamentous cord insertion (adjusted RR (aRR), 2.11 (95% CI, 1.65-2.60)), cord knots (aRR, 1.53 (95% CI, 1.15-2.04)) and placental abnormalities (placenta previa (aRR, 3.03 (95% CI, 2.00-4.61)), placental abruption (aRR, 10.63 (95% CI, 8.57-13.18)) and retained placenta (aRR, 1.71 (95% CI, 1.32-2.22))) carried an increased risk of CP. Velamentous cord insertion was associated with CP regardless of gestational age or sex. A retained placenta was associated with a 2-fold increased risk for CP in males, while the associations of SUA and cord knot with CP were significant only among females.

CONCLUSIONS

The detection of placental and umbilical cord abnormalities may help identify children at increased risk of CP. The associations between placental or umbilical cord abnormalities and the risk of CP do not vary substantially with gestational age at birth or sex of the child. © 2023 The Authors. Ultrasound in Obstetrics & Gynecology published by John Wiley & Sons Ltd on behalf of International Society of Ultrasound in Obstetrics and Gynecology.

An approximation method for the prevention of knot formation during catheterization in children

INTRODUCTION

Knotting during urethral catheterization in children is an unpleasant situation. We aimed to minimize this risk.

METHOD

To prevent knot formation, we must understand its nature. We focused on the simplest, and most fundamental, known as overhand knot.

RESULTS

Calculating the maximum length of catheter inserted in the bladder without risk of knotting, we estimated the minimum length of catheter needed for an overhand knot.

DISCUSSION

This theoretical approach provides a rough estimation which may contribute to secure catheterization.

CONCLUSION

Adding the calculated length to the appropriate for gender and age urethral length, may reduce knotting risk.

Strengthening Timber Structural Members with CFRP and GFRP: A State-of-the-Art Review

The application of fibre-reinforced polymers (FRP) for strengthening timber structures has proven its efficiency in enhancing load-bearing capacity and, in some cases, the stiffness of structural elements, thus providing cost-effective and competitive alternatives both in new design and retrofitting existing historical buildings. Over the last few decades, several reinforcing materials and techniques evolved, and considerable progress was made in numerical modelling, especially using the finite element method. As this field of research has become extensive and diversified, as well as numerous contradicting results have emerged, a thorough review is necessary. This manuscript covers the topics of historical preliminaries, reinforcing with carbon and glass fibre composites, bond characteristics, main reinforcing techniques, modelling of knots, and the effects of the fibre waviness on the composite behaviour. A detailed overview is given on the experimental and numerical investigation of mechanics of strengthened beams. A one-of-a-kind table is presented that compares the stiffness improvement observed in several studies with analytical estimates. Attention is drawn to a number of challenges that have arisen, e.g., the moderate stiffness enhancement, composite-to-wood interface, modelling of knots, and strengthening of defected timber members. This paper can be used as a starting point for future research and engineering projects.

Channels with Helical Modulation Display Stereospecific Sensitivity for Chiral Superstructures

By means of coarse-grained molecular dynamics simulations, we explore chiral sensitivity of confining spaces modelled as helical channels to chiral superstructures represented by polymer knots. The simulations show that helical channels exhibit stereosensitivity to chiral knots localized on linear chains by effect of external pulling force and also to knots embedded on circular chains. The magnitude of the stereoselective effect is stronger for torus knots, the effect is weaker in the case of twist knots, and amphichiral knots do exhibit no chiral effects. The magnitude of the effect can be tuned by the so-far investigated radius of the helix, the pitch of the helix and the strength of the pulling force. The model is aimed to simulate and address a range of practical situations that may occur in experimental settings such as designing of nanotechnological devices for the detection of topological state of molecules, preparation of new gels with tailor made stereoselective properties, or diffusion of knotted DNA in biological conditions.

Knots Tied With High-Tensile Strength Tape Biomechanically Outperform Knots Tied With Round Suture

Background

Tape-type suture material is well-accepted in arthroscopy surgery.

Purpose

To compare the knot security of a high-tensile strength round suture and high-tensile strength tape with commonly used arthroscopic knots.

Study Design

Controlled laboratory study.

Methods

We compared the performance of No. 2 braided nonabsorbable high-strength suture with that of 1.3-mm braided nonabsorbable high-strength tape. Five commonly used arthroscopic knots were investigated: the Roeder knot; the Western knot; the Samsung Medical Center (SMC) knot; the Tennessee knot; and a static surgeon's knot. Seven knots were tied for each combination of knots and suture types. Knots were tied on a 30-mm circumferential metal post, and the suture loops were transferred to a materials testing machine. After preloading to 5 N, all specimens were loaded to failure. The clinical failure load, defined as the maximal force to failure at 3 mm of crosshead displacement, yield load, and stiffness, were recorded. A 2-way analysis of variance was used to determine differences between the groups.

Results

Both suture type and knot type significantly affected the clinical failure load, yield load, and stiffness (P = .002). The high-strength tape resulted in a significantly greater clinical failure load than the high-strength suture in the case of the Roeder knot, Western knot, and SMC knot (P = .027, .005, and .016, respectively). When the high-strength round suture was used, the Roeder knot, Western knot, and SMC knot resulted in significantly smaller clinical failure loads compared with the Tennessee knot (P = .011, .003, and .035, respectively) and the static surgeon's knot (P < .001 for all). When the high-strength tape was used, the Roeder knot, Western knot, and SMC knot resulted in significantly smaller clinical failure loads compared with the static surgeon's knot (P = .001, .001, and .003, respectively).

Conclusion

The results of this study indicated that arthroscopic knots tied using 1.3-mm high-strength tape biomechanically outperformed knots tied using a No. 2 high-strength suture. While the static surgeon's knot exhibited the best biomechanical properties, the Tennessee knot resulted in generally better biomechanical properties among the arthroscopic sliding knots.

Clinical Relevance

Elongation and loosening of tied knots possibly affects the clinical results of repaired constructs.

Suture Slippage After Arthroscopic Cuff Repair: Medial Displacement of Suture Knots on Follow-up Ultrasonography

Background:

Compared with the single-row technique, the double-row rotator cuff repair technique is known to have a higher load to failure and a lower frequency of gap formation, leading to a lower retear rate. There are some patients with poor clinical outcomes or poor muscle strength without radiologic retear.

Purpose/Hypothesis:

To assess the postoperative position of suture knots via serial ultrasonography in patients who had undergone arthroscopic rotator cuff repair with the suture-bridge technique. Our hypothesis was that the suture would pull out of the lateral anchor (suture slippage), changing the positions of the medial suture knots during healing.

Study Design:

Case series; Level of evidence, 4.

Methods:

This study included 53 patients (55 shoulders) who underwent arthroscopic suture-bridge repair and were evaluated for a minimum of 24 months. On serial ultrasonography, a straight line was drawn between the top of the greater tuberosity and the medial cortex of the anchor hole. The distances between the knots of the medial rows and the perpendicular line through the center of the anchor hole were measured in longitudinal plane images of the supraspinatus. Follow-up ultrasonography was performed at 2, 3, and 6 months postoperatively as well as at the final visit. The visual analog scale, the American Shoulder and Elbow Surgeons score, the Constant score, and the University of California, Los Angeles shoulder score were recorded preoperatively and on the final follow-up.

Results:

Of the 55 shoulders, 6 developed retears at repaired sites. The mean follow-up duration was 37.5 months (range, 24-65 months). Slippage distance increased significantly over time (P < .001). The slippage at the final visit did not differ between patients with retear and no retear (13.4 mm for retear group; 10.6 mm for no retear group [P = .096]).

Conclusion:

Suture knots of the medial row migrated medially via a suture pullout from the lateral row anchor of suture-bridge technique. Suture slippage distance did not differ significantly between retear and no retear groups.

Topoly: Python package to analyze topology of polymers

The increasing role of topology in (bio)physical properties of matter creates a need for an efficient method of detecting the topology of a (bio)polymer. However, the existing tools allow one to classify only the simplest knots and cannot be used in automated sample analysis. To answer this need, we created the Topoly Python package. This package enables the distinguishing of knots, slipknots, links and spatial graphs through the calculation of different topological polynomial invariants. It also enables one to create the minimal spanning surface on a given loop, e.g. to detect a lasso motif or to generate random closed polymers. It is capable of reading various file formats, including PDB. The extensive documentation along with test cases and the simplicity of the Python programming language make it a very simple to use yet powerful tool, suitable even for inexperienced users. Topoly can be obtained from https://topoly.cent.uw.edu.pl.

Signaling Mechanism of Phytochromes in Solution

Phytochrome proteins guide the red/far-red photoresponse of plants, fungi, and bacteria. Crystal structures suggest that the mechanism of signal transduction from the chromophore to the output domains involves refolding of the so-called PHY tongue. It is currently not clear how the two other notable structural features of the phytochrome superfamily, the so-called helical spine and a knot in the peptide chain, are involved in photoconversion. Here, we present solution NMR data of the complete photosensory core module from Deinococcus radiodurans. Photoswitching between the resting and the active states induces changes in amide chemical shifts, residual dipolar couplings, and relaxation dynamics. All observables indicate a photoinduced structural change in the knot region and lower part of the helical spine. This implies that a conformational signal is transduced from the chromophore to the helical spine through the PAS and GAF domains. The discovered pathway underpins functional studies of plant phytochromes and may explain photosensing by phytochromes under biological conditions.

An intra-aortic guide wire: what "knot" to do

We report a rare complication of central venous catheter placement in a 5-month-old baby.

Case report

Small-bowel obstruction (SBO) and volvulus as a result of ventriculoperitoneal shunting are a rare phenomenon, especially when resulting in bowel necrosis. The authors report the rare event of SBO, bowel strangulation, and necrosis in a pediatric patient after the abdominal catheter became knotted around his small bowel, and they provide a comprehensive review of the literature. The authors argue that shunt configuration is an important consideration for a patient presenting with SBO, and that symptomatic shunt knotting is a reason for surgical correction.

Anatomic Knot Suture Anchor Versus Knotless Suture Anchor Technique for Anterior Talofibular Ligament Repair: A Biomechanical Comparison

Background:

To date, there are few biomechanical studies comparing the strength between knot repair and knotless repair procedures for anterior talofibular ligament (ATFL) injury.

Purpose:

To perform a biomechanical comparison of the strength of the arthroscopic ATFL repair technique with knot or knotless suture anchors in a cadaveric model with partial or complete ATFL injuries.

Study Design:

Controlled laboratory study.

Methods:

A total of 24 fresh-frozen cadaveric ankles were used. Arthroscopy was used to identify, section, and repair the ATFL on the fibular insertion site. The specimens were then randomly placed into 1 of 4 groups: group A received complete ATFL section and 1–suture anchor repair with knot, group B received complete ATFL section and 1-anchor knotless repair, group C received partial ATFL section and 1–suture anchor repair with knot, and group D received partial ATFL section and 1-anchor knotless repair. After repair, the ATFL tension was measured first with a digitalized tensiometer. Specimens were then mounted on a materials testing system to determine the ultimate load to failure and stiffness.

Results:

The mean ± SD ligament tension measured during the arthroscopic procedure was 8.6 ± 0.6 N for group A, 9.2 ± 0.5 N for group B, 9.4 ± 1.1 N for group C, and 9.6 ± 0.9 N for group D. No significant difference in tension was detected among groups. In load-to-failure testing, the mean ultimate failure load was 27.9 ± 4.1 N for group A, 26.2 ± 9.3 N for group B, 81.9 ± 26.5 N for group C, and 88.1 ± 41.6 N for group D. The mean ultimate failure loads of the partial repair groups were significantly higher than those of the complete repair groups (C vs A, P = .008; D vs B, P = .002), while there was no significant difference between groups A and B (P > .05) or between groups C and D (P > .05).

Conclusion:

The results of the present study showed that there was no significant difference in biomechanical properties between knot repair and knotless repair techniques.

Clinical Relevance:

Biomechanically, the results showed that knot suture anchor and knotless suture repair provide similar biomechanical strength for ATFL injury. Unfortunately, these methods in the complete ATFL section models provided less than half the strength and stiffness in the partial ATFL section models at time zero after surgery. As a result, 1–suture anchor repair is not suitable for complete ATFL injury regardless of the repair method.

Knot my problem: Overcoming transradial catheter complications

Not all complications from transradial access can be prevented, even with diligent patient selection and preprocedure planning. This brief visual report offers technical suggestions to reverse knots and kinks encountered during catheter manipulation for endovascular transradial cerebral procedures.

Does Medial-Row Fixation Technique Affect the Retear Rate and Functional Outcomes After Double-Row Transosseous-Equivalent Rotator Cuff Repair?

Background:

Double-row transosseous-equivalent (TOE) rotator cuff repair techniques have been widely accepted because of their superior biomechanical properties when compared with arthroscopic single-row repair. Concerns regarding repair overtensioning with medial-row knot tying have led to increased interest in knotless repair techniques; however, there is a paucity of clinical data to guide the choice of technique.

Hypothesis:

Arthroscopic TOE repair techniques using knotless medial-row fixation will demonstrate lower retear rates and greater improvements in the Constant score relative to conventional knot-tying TOE techniques.

Study Design:

Systematic review; Level of evidence, 4.

Methods:

A systematic review of 3 databases (PubMed, Cochrane, and Embase) was performed using PRISMA (Preferred Reporting Items for Systematic Meta-Analyses) guidelines. Inclusion criteria were English-language studies that examined repair integrity or Constant scores after arthroscopic rotator cuff repair with TOE techniques. Two investigators independently screened results for relevant articles. Data regarding the study design, surgical technique, retear rate, and Constant shoulder score were extracted from eligible studies. A quality assessment of all articles was performed using the Methodological Index for Non-Randomized Studies (MINORS) criteria.

Results:

The systematic review identified a total of 32 studies (level of evidence, 1-4) that met inclusion and exclusion criteria. Of the 32 studies, 5 reported on knotless TOE techniques, 25 reported on knot-tying TOE techniques, and 2 reported on both. In the knotless group, retear rates ranged from 6% to 36%, and Constant scores ranged from 38-65 (preoperative) to 73-83 (postoperative). In the knot-tying group, retear rates ranged from 0% to 48%, and Constant scores ranged from 42-64 (preoperative) to 55-96 (postoperative).

Conclusion:

Despite several theoretical advantages of knotless TOE repair, both knotless and knot-tying techniques reported considerable improvement in functional outcomes after rotator cuff repair. Although tendon failure rates showed a downward trend in knotless studies, additional prospective studies are warranted to better understand the role of medial-row fixation on tendon repair integrity and postoperative clinical outcomes.

Biomechanical comparison of modified Lim/Tsai tendon repairs with intra- and extra-tendinous knots

We compared the Lim/Tsai tendon repair technique using an extra-tendinous knot with modification using an intra-tendinous knot. The ultimate tensile strength, load to 2 mm gap force, stiffness, mode of failure, location of failure, and time taken to repair each tendon were recorded during a single cycle loading test in 20 tendons with each repair method. We found that the ultimate tensile strength and 2 mm gap force of the modified Lim/Tsai repair with an extra-tendinous knot (56 SD 5 N and 14 SD 2 N, respectively) were statistically significantly higher than that of the modified Lim/Tsai repair with intra-tendinous knot (51 SD 7 N and 11 SD 2 N, respectively). We conclude that the modified Lim/Tsai repair with extra-tendinous knot is stronger, despite having the same number of core strands.

Reduction of catheter kinks and knots via radial approach

Coronary angiography and percutaneous coronary intervention using the radial approach are becoming more frequent. Pronounced guide catheter manipulation in cases with tortuous access routes may lead to severe catheter kinking or knotting. The purpose of this review article is to present several techniques to resolve radial access catheter knots and kinks. First, simple maneuvers such as gentle traction, rotation, and guidewire advancement can often resolve minor kinking; however, complex loops and kinks are often not reversible with these simple maneuvers. Second, fixing the distal catheter tip using external compression, encasing the knot with a larger sheath, or untwisting the knot with hydraulic pressure can be useful. Finally, internal fixation by grasping the kinked catheter with a snare introduced via the femoral artery allows both ends of the catheter to be rotated in opposite directions to untwist the catheter for safe removal.

A Modified Tie Technique for Securing Endotracheal Tubes

BACKGROUND

Unintentional extubation is a well-documented and potentially life-threatening phenomenon. There is little research into the factors that lead to unintentional extubation, and therefore how to prevent it. Endotracheal tubes (ETTs) are commonly secured with 1 cm twill tape, but there is little evidence on how to best tie them in place. We have devised a new knot for securing these tubes in place, and we have assessed its degree of slippage when exposed to both perpendicular and sliding forces in comparison with other commonly used knots.

METHODS

We constructed a weighted apparatus to test the effects of these forces and measure whether conventional ETTs slipped. We tested the knots both wet and dry to better simulate the clinical environment. We also conducted a manual manipulation test in which a single operator attempted to slide the knot along the ETT. Each knot was tested 10 times for the weight test under both wet and dry conditions, and 8 times for the slip test.

RESULTS

The normal knot slipped when weighted both wet and dry, while the clove hitch failed the weight test only when wet. Both the modified cow hitch and double hitch withstood all weights. Only the double hitch did not slip under any circumstances on either test.

CONCLUSIONS

The new double hitch was superior to all conventional knots tested. It did not slip under any conditions and therefore may be of use to prevent unintentional extubation, particularly in the ICU setting.

Arthroscopic Knot Removal for Failed Superior Labrum Anterior-Posterior Repair Secondary to Knot-Induced Pain

BACKGROUND

Studies on failed superior labrum anterior-posterior (SLAP) repair are increasing. However, the number of reports on treatment options for failed SLAP repair remains quite low, and the clinical results vary between different study groups.

PURPOSE

To describe the clinical presentation of failed SLAP repair due to knot-induced pain and evaluate the efficacy of arthroscopic knot removal.

STUDY DESIGN

Case series; Level of evidence, 4.

METHODS

The authors retrospectively reviewed records of 11 patients (mean age, 24.6 ± 8.6 years; range, 17-43 years) with stable, healed SLAP lesions with knot-induced pain after arthroscopic fixation of unstable type II SLAP lesions. All patients demonstrated a positive compression-rotation test before knot removal. The mean follow-up duration after knot removal was 48.0 ± 37.4 months (range, 24-156 months). The mean duration between primary fixation and knot removal was 21.2 ± 14.7 months (range, 8-56 months).

RESULTS

Sharp pain (100%) and clicking (64%) were the most common symptoms. The knot was positioned on the glenoid side in 5 patients and the labral side in 6 patients. The knots on the glenoid side had associated humeral head cartilage damage. The mean University of California at Los Angeles score significantly improved from 15.2 points to 31.7 points after knot removal ( P = .003) Additionally, the mean Constant score greatly improved from a mean of 56.5 points to 89.8 points ( P = .003). At a mean of 3 weeks after surgery, we observed dramatic pain relief. Six weeks after surgery, the compression-rotation test was negative in all patients.

CONCLUSION

The most common symptom of knot-induced pain after SLAP repair was persistent sharp pain followed by clicking. The knot appears to be a cause of pain in failed SLAP repairs, and arthroscopic knot removal can provide dramatic pain relief and significant improvement of clinical outcomes.

Knotted fields and explicit fibrations for lemniscate knots

We give an explicit construction of complex maps whose nodal lines have the form of lemniscate knots. We review the properties of lemniscate knots, defined as closures of braids where all strands follow the same transverse (1, ℓ) Lissajous figure, and are therefore a subfamily of spiral knots generalizing the torus knots. We then prove that such maps exist and are in fact fibrations with appropriate choices of parameters. We describe how this may be useful in physics for creating knotted fields, in quantum mechanics, optics and generalizing to rational maps with application to the Skyrme-Faddeev model. We also prove how this construction extends to maps with weakly isolated singularities.

Statistical and Dynamical Properties of Topological Polymers with Graphs and Ring Polymers with Knots

We review recent theoretical studies on the statistical and dynamical properties of polymers with nontrivial structures in chemical connectivity and those of polymers with a nontrivial topology, such as knotted ring polymers in solution. We call polymers with nontrivial structures in chemical connectivity expressed by graphs "topological polymers". Graphs with no loop have only trivial topology, while graphs with loops such as multiple-rings may have nontrivial topology of spatial graphs as embeddings in three dimensions, e.g., knots or links in some loops. We thus call also such polymers with nontrivial topology "topological polymers", for simplicity. For various polymers with different structures in chemical connectivity, we numerically evaluate the mean-square radius of gyration and the hydrodynamic radius systematically through simulation. We evaluate the ratio of the gyration radius to the hydrodynamic radius, which we expect to be universal from the viewpoint of the renormalization group. Furthermore, we show that the short-distance intrachain correlation is much enhanced for real topological polymers (the Kremer⁻Grest model) expressed with complex graphs. We then address topological properties of ring polymers in solution. We define the knotting probability of a knot K by the probability that a given random polygon or self-avoiding polygon of N vertices has the knot K. We show a formula for expressing it as a function of the number of segments N, which gives good fitted curves to the data of the knotting probability versus N. We show numerically that the average size of self-avoiding polygons with a fixed knot can be much larger than that of no topological constraint if the excluded volume is small. We call it "topological swelling".

Helicity conservation and twisted Seifert surfaces for superfluid vortices

Starting from the continuum definition of helicity, we derive from first principles its different contributions for superfluid vortices. Our analysis shows that an internal twist contribution emerges naturally from the mathematical derivation. This reveals that the spanwise vector that is used to characterize the twist contribution must point in the direction of a surface of constant velocity potential. An immediate consequence of the Seifert framing is that the continuum definition of helicity for a superfluid is trivially zero at all times. It follows that the Gauss-linking number is a more appropriate definition of helicity for superfluids. Despite this, we explain how a quasi-classical limit can arise in a superfluid in which the continuum definition for helicity can be used. This provides a clear connection between a microscopic and a macroscopic description of a superfluid as provided by the Hall-Vinen-Bekarevich-Khalatnikov equations. This leads to consistency with the definition of helicity used for classical vortices.

Transfer RNA methyltransferases with a SpoU-TrmD (SPOUT) fold and their modified nucleosides in tRNA

The existence of SpoU-TrmD (SPOUT) RNA methyltransferase superfamily was first predicted by bioinformatics. SpoU is the previous name of TrmH, which catalyzes the 2’-O-methylation of ribose of G18 in tRNA; TrmD catalyzes the formation of N¹-methylguanosine at position 37 in tRNA. Although SpoU (TrmH) and TrmD were originally considered to be unrelated, the bioinformatics study suggested that they might share a common evolution origin and form a single superfamily. The common feature of SPOUT RNA methyltransferases is the formation of a deep trefoil knot in the catalytic domain. In the past decade, the SPOUT RNA methyltransferase superfamily has grown; furthermore, knowledge concerning the functions of their modified nucleosides in tRNA has also increased. Some enzymes are potential targets in the design of anti-bacterial drugs. In humans, defects in some genes may be related to carcinogenesis. In this review, recent findings on the tRNA methyltransferases with a SPOUT fold and their methylated nucleosides in tRNA, including classification of tRNA methyltransferases with a SPOUT fold; knot structures, domain arrangements, subunit structures and reaction mechanisms; tRNA recognition mechanisms, and functions of modified nucleosides synthesized by this superfamily, are summarized. Lastly, the future perspective for studies on tRNA modification enzymes are considered.

Trapping a Knot into Tight Conformations by Intra-Chain Repulsions

Knots can occur in biopolymers such as DNA and peptides. In our previous study, we systematically investigated the effects of intra-chain interactions on knots and found that long-range repulsions can surprisingly tighten knots. Here, we use this knowledge to trap a knot into tight conformations in Langevin dynamics simulations. By trapping, we mean that the free energy landscape with respect to the knot size exhibits a potential well around a small knot size in the presence of long-range repulsions, and this potential can well lead to long-lived tight knots when its depth is comparable to or larger than thermal energy. We tune the strength of intra-chain repulsion such that a knot is weakly trapped. Driven by thermal fluctuations, the knot can escape from the trap and is then re-trapped. We find that the knot switches between tight and loose conformations-referred to as "knot breathing". We use a Yukawa potential to model screened electrostatic interactions to explore the relevance of knot trapping and breathing in charged biopolymers. We determine the minimal screened length and the minimal strength of repulsion for knot trapping. We find that Coulomb-induced knot trapping is possible to occur in single-stranded DNA and peptides for normal ionic strengths.

A Syndromic Neurodevelopmental Disorder Caused by De Novo Variants in EBF3

Early B cell factor 3 (EBF3) is a member of the highly evolutionarily conserved Collier/Olf/EBF (COE) family of transcription factors. Prior studies on invertebrate and vertebrate animals have shown that EBF3 homologs are essential for survival and that loss-of-function mutations are associated with a range of nervous system developmental defects, including perturbation of neuronal development and migration. Interestingly, aristaless-related homeobox (ARX), a homeobox-containing transcription factor critical for the regulation of nervous system development, transcriptionally represses EBF3 expression. However, human neurodevelopmental disorders related to EBF3 have not been reported. Here, we describe three individuals who are affected by global developmental delay, intellectual disability, and expressive speech disorder and carry de novo variants in EBF3. Associated features seen in these individuals include congenital hypotonia, structural CNS malformations, ataxia, and genitourinary abnormalities. The de novo variants affect a single conserved residue in a zinc finger motif crucial for DNA binding and are deleterious in a fly model. Our findings indicate that mutations in EBF3 cause a genetic neurodevelopmental syndrome and suggest that loss of EBF3 function might mediate a subset of neurologic phenotypes shared by ARX-related disorders, including intellectual disability, abnormal genitalia, and structural CNS malformations.

Intravesical catheter knotting: an unusual complication of suprapubic catheterization

Suprapubic catheterization is commonly used to drain urine temporarily from the bladder. Although it is a commonly performed procedure, it is not without complications. Many of these complications related to surgical technique. However, some unpredictable complications are related to the catheter itself. Intravesical catheter knotting is a very rare event and usually has been reported in feeding catheters used as an urethral catheter. We report a case of a suprapubic Cystofix catheter knot, removed by sustained traction. This complication was probably due to an excessive length of catheter having been inserted into the bladder, thus forming redundant loops that increased the risk of bending onto itself.

Ventriculoperitoneal shunt with a rare twist: small-bowel ischemia and necrosis secondary to knotting of peritoneal catheter

Small-bowel ischemia and necrosis due to knotting of the peritoneal catheter is an extremely rare complication related to a ventriculoperitoneal shunt (VPS). A 3-month-old girl, with a history of Chiari II malformation and myelomeningocele (MM) after undergoing right occipital VPS insertion and MM repair at birth, presented to the emergency department with a high-grade fever. Examination of a CSF sample obtained via shunt tap raised suspicion for the presence of infection. Antibiotic therapy was initiated, and subsequently the VPS was removed and an external ventricular drain was placed. Intraoperatively, as attempts at pulling the distal catheter from the scalp incision were met with resistance, the distal catheter was cut and left in the abdomen while the remainder of the shunt system was successfully removed. While the patient was awaiting definitive shunt revision surgery to replace the VPS, she developed abdominal distension due to small-bowel obstruction. An emergency exploratory laparotomy revealed a knot in the distal catheter looping around and strangulating the distal ileum, causing small-bowel ischemia and necrosis in addition to the obstruction. A small-bowel resection with ileostomy was performed, with subsequent placement of ventriculoatrial shunt for treatment of hydrocephalus. The authors report this exceedingly rare clinical scenario to highlight the fact that any retained distal catheter must be carefully managed with immediate abdominal exploration to remove the distal catheter to avoid bowel necrosis as pulling of a knotted peritoneal catheter may strangulate the bowel and cause ischemia, with significant clinical morbidity and possible mortality.

A knot in the protein structure - probing the near-infrared fluorescent protein iRFP designed from a bacterial phytochrome

The possibility of engineering near-infrared fluorescent proteins and biosensors from bacterial phytochrome photoreceptors (BphPs) has led to substantial interest in this family of proteins. The near-infrared fluorescent proteins have allowed non-invasive bio-imaging of deep tissues and whole organs in living animals. BphPs and derived near-infrared fluorescent proteins contain a structural element, called a knot, in their polypeptide chains. The formation of knot structures in proteins was refuted for a long time. Here, we studied the denaturation and renaturation processes of the near-infrared fluorescent probe iRFP, engineered from RpBphP2, which utilizes a heme-derived tetrapyrrole compound biliverdin as a chromophore. iRFP contains a unique figure-of-eight knot. The denaturation and renaturation curves of the iRFP apoform coincided well, suggesting efficient refolding. However, the iRFP holoform exhibited irreversible unfolding and aggregation associated with the bound chromophore. The knot structure in the apoform did not prevent subsequent binding of biliverdin, resulting in the functional iRFP holoform. We suggest that the irreversibility of protein unfolding is caused by post-translational protein modifications, such as chromophore binding, rather than the presence of the knot. These results are essential for future design of BphP-based near-infrared probes, and add important features to our knowledge of protein folding.

Suspension without a knot in the noose

Most deaths by hanging are due to self-suspension. This may be carried out by a wide variety of methods, but a typical method of self-suspension is to attach a thin rope to a high point such as a ceiling beam. A 35-year-old woman committed suicide by hanging, where the ligature employed was not a typical knotted noose but instead an open iron chain anchored to the ceiling above.

Combined molecular algorithms for the generation, equilibration and topological analysis of entangled polymers: methodology and performance

We review the methodology, algorithmic implementation and performance characteristics of a hierarchical modeling scheme for the generation, equilibration and topological analysis of polymer systems at various levels of molecular description: from atomistic polyethylene samples to random packings of freely-jointed chains of tangent hard spheres of uniform size. Our analysis focuses on hitherto less discussed algorithmic details of the implementation of both, the Monte Carlo (MC) procedure for the system generation and equilibration, and a postprocessing step, where we identify the underlying topological structure of the simulated systems in the form of primitive paths. In order to demonstrate our arguments, we study how molecular length and packing density (volume fraction) affect the performance of the MC scheme built around chain-connectivity altering moves. In parallel, we quantify the effect of finite system size, of polydispersity, and of the definition of the number of entanglements (and related entanglement molecular weight) on the results about the primitive path network. Along these lines we approve main concepts which had been previously proposed in the literature.