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Although deep learning has revolutionized protein structure prediction, almost all experimentally characterized de novo protein designs have been generated using physically based approaches such as Rosetta. Here, we describe a deep learning–based protein sequence design method, ProteinMPNN, that has outstanding performance in both in silico and experimental tests. On native protein backbones, ProteinMPNN has a sequence recovery of 52.4% compared with 32.9% for Rosetta. The amino acid sequence at different positions can be coupled between single or multiple chains, enabling application to a wide range of current protein design challenges. We demonstrate the broad utility and high accuracy of ProteinMPNN using x-ray crystallography, cryo–electron microscopy, and functional studies by rescuing previously failed designs, which were made using Rosetta or AlphaFold, of protein monomers, cyclic homo-oligomers, tetrahedral nanoparticles, and target-binding proteins.

Background: Endocrine therapy (ET) is the standard of care for treatment of HR+, HER2– aBC. However, ET resistance occurs frequently leading to disease progression. Dysregulation of the PI3K/AKT/mTOR pathway, specifically mutations in PIK3CA, the gene encoding the p110alpha subunit of PI3K, has been implicated in ET resistance. In a phase 1 study, alpelisib, a PI3Kα-specific inhibitor, in combination with fulvestrant has shown antitumor activity in patients with PIK3CA mutant, HR+, HER2– aBC. The present BYLieve (NCT03056755) study aims to assess the efficacy and safety of alpelisib + fulvestrant/letrozole in PIK3CA-mutant, HR+, HER2– aBC progressing on/after prior CDK4/6 inhibitor (CDK4/6i) therapy. Methods: BYLieve is a phase 2, multicenter, open-label, 2-cohort, non-comparative study. Men and postmenopausal women (≥ 18 years) with PIK3CA-mutant, HR+, HER2− locally advanced or metastatic breast cancer that has progressed on/after prior CDK4/6i therapy are eligible. Other eligibility criteria include ≥ 1 measurable lesion (RECIST v1.1) or predominantly lytic bone lesion; ECOG PS ≤ 2; and no prior PI3K inhibitor therapy. Patients are allocated to 2 cohorts based on the prior ET partner (aromatase inhibitor (AI) or fulvestrant) used in combination with CDK4/6i. Cohort A (patients who had received CDK4/6i + AI): oral alpelisib (300 mg once daily) + intramuscular fulvestrant (500 mg on days 1 and 15 of cycle 1, and day 1 of cycles ≥ 2 [28-day cycles]) and cohort B (patients who had received CDK4/6i + fulvestrant): oral alpelisib (300 mg once daily) + oral letrozole (2.5 mg once daily). Study treatment will continue until disease progression or intolerable toxicity. The primary end point is the proportion of patients who are alive without disease progression at 6 months (RECIST v1.1; local assessment), which will be evaluated separately in each cohort and presented together with 2-sided 90% confidence intervals using Clopper and Pearson (1934) exact method. Evidence of treatment effect will be demonstrated if the lower bound of the 90% CI is greater than 30%. A total sample size of 80 patients in each cohort is planned. Secondary end points include progression-free survival (PFS), PFS on next-line treatment (PFS2), overall response rate, clinical benefit rate, duration of response, safety, and tolerability. Detection of frequency of PIK3CA mutations in ctDNA and its correlation with response is an exploratory end point. Citation Format: Rugo HS, Turner N, Chia S, Ciruelos E, Nienstedt C, Ridolfi A, Kong O, Sankaran B, Juric D. BYLieve: A phase 2 study of alpelisib with fulvestrant or letrozole for treatment of PIK3CA mutant, hormone receptor-positive (HR+), human epidermal growth factor receptor 2-negative (HER2–) advanced breast cancer (aBC) progressing on/after cyclin-dependent kinase (CDK)4/6 inhibitor therapy [abstract]. In: Proceedings of the 2017 San Antonio Breast Cancer Symposium; 2017 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2018;78(4 Suppl):Abstract nr OT3-05-02.

X-ray diffraction and reflectivity, X-ray photoelectron spectroscopy and spectroscopic ellipsometry were applied to study the initial composition, thickness, lattice structure and refractive index of ‘fresh’ and annealed thin SiOx films (∼15 nm) on crystalline silicon substrates, prepared by thermal evaporation of SiO in vacuum. It has been ascertained that the film thickness and composition (x = 1.3) of the ‘fresh’ films are very close to the values set during the deposition. It has been shown that furnace annealing of the films at 1000 °C causes phase separation, film densification and small modification of the Si–SiOx interface. Transmission electron microscopy results have proven that a self-assembling process leads to formation of Si nanocrystals with a diameter of ∼4–5 nm and to epitaxial overgrowth of the Si substrate, increasing the c-Si/SiOx interface transition region to 6–7 monolayers. The nanocrystals are randomly distributed in an amorphous SiO2 matrix being closer to the Si–SiOx interface. Formation of tunnel oxide layer with a thickness of 3–5 nm has been found upon annealing. Clockwise hysteresis has been observed in the capacitance-voltage characteristics measured which has been explained by assuming charging and discharging of the nanocrystals with holes, which tunnel from the Si substrate.

Estrogen-receptor positive (ER+) breast cancers make up approximately 70% of all breast cancers diagnosed. While patients with ER+ breast cancer have a better prognosis than other subtypes of breast cancer, the majority of those with advanced metastatic disease will eventually relapse. This has been attributed, in part, to mutations in the ER gene that result in constitutive activation of ER and contribute to aromatase inhibitor treatment resistance. As a strategy to deliver a more durable response in this setting, the use of selective estrogen receptor degraders (SERDs) that target and inhibit both wild-type and mutant ER has gained widespread attention. Indeed, fulvestrant, the only approved SERD on the market, is currently used as a second-line therapy in the metastatic setting, however, the intramuscular route of administration and pharmacokinetic properties of fulvestrant have fueled the development of orally bioavailable SERDs. We have previously described elacestrant (RAD1901), a novel and orally bioavailable selective estrogen receptor degrader (SERD) as an inhibitor of ER+ breast cancer growth in preclinical models, including those that harbor ER mutations and those that are insensitive to fulvestrant. In addition to ER mutations, the activation of parallel oncogenic pathways can also drive endocrine resistance, with the PI3K/Akt/mTOR pathway chief among those driving growth and treatment resistance to endocrine therapy. Consistent with these above-mentioned findings, recent clinical strategies to treat advanced ER+ disease have involved combining SERDs with PI3K inhibitors. Alpelisib (BYL-719) is a PI3K-alpha specific inhibitor that is being developed in combination with endocrine agents for the treatment of ER+ breast cancer. Here, we examined the effect of elacestrant in combination with alpelisib, in two ER+ breast cancer PDX models (one harboring wild-type ER and one harboring a Y537S mutation in the ER gene). The combination of elacestrant (10mg/kg) and alpelisib (35mg/kg) was well tolerated and resulted in significant tumor growth inhibition in both PDX models. Interestingly, in the mutant ER PDX model, the combination resulted in significantly greater growth inhibition relative to either compound alone. These data suggest the dual inhibition of the ER and PI3K signaling pathways with elacestrant and alpelisib produces significant anti-tumor activity in clinically-relevant PDX models, including those harboring ER mutations. Citation Format: Sankaran B, Garner F, Hattersley G, Purandare D, Bihani T. Anti-tumor activity of elacestrant (RAD1901) in combination with alpelisib (BYL-719) in patient-derived xenograft models of ER+ breast cancer [abstract]. In: Proceedings of the 2017 San Antonio Breast Cancer Symposium; 2017 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2018;78(4 Suppl):Abstract nr P4-04-14.

The binding behavior of lumiflavin, a biologically vital ligand, with DNA duplexes containing an abasic (AP) site and various target nucleobases opposite the AP site is studied. Lumiflavin binds selectively to thymine (T) opposite the AP site in a DNA duplex over other nucleobases. Using 1H NMR spectroscopy and fluorescence measurements, we show that ligand-DNA complexation takes place by hydrogen-bond formation between the ligand and the target nucleobases and by stacking interactions between the ligand and the nucleobases flanking the AP site. From isothermal titration calorimetric experiments, we find that ligand incorporation into the AP sites is primarily enthalpy-driven. Examination of ionic strength dependency of ligand binding with DNA reveals that ligand-DNA complexation is a manifestation of both electrostatic and nonelectrostatic interactions and that the contribution from the nonelectrolyte effect is fundamental for the stabilization of the ligand-DNA complex. In comparison to riboflavin, reported previously as a T-selective ligand, lumiflavin binds to the DNA much more strongly and is a more promising ligand for efficient detection of T-related single nucleotide polymorphisms.

Single-nucleotide polymorphism analysis based on fabrication of the abasic site (AP site) in the thiolated DNA duplexes is demonstrated. The AP site allows an electrochemical indicator to bind to target nucleotides accompanied by electrochemical signaling and to detect a specific nucleobase of a target nucleic acid. A mixed self-assembled monolayer of thiolated AP site-containing probe DNA is hybridized with the target DNA so as to direct the AP site toward the target nucleobase. In this way, hydrophobic microenvironments are provided for the electrochemical indicator to recognize the specific nucleobase on the DNA duplex based on the difference in the electrochemical response. The electrochemical response is found to be strengthened at low temperature. The enhanced electrochemical response of riboflavin induced by temperature in an AP site-containing DNA duplex is used to detect thymidine specifically based on an electrochemical approach. Keywords: Riboflavin, Abasic site, Electrochemical detection, Square wave voltammetry, Biosensor, Single-nucleotide polymorphisms

Synthesis, photophysical behaviour and metal ion signalling ability of 3-component systems, I and II, comprising a 4-aminophthalimido moiety as fluorophore, a dimethylene spacer and two different azacrown receptors, are reported. The fluorescence quantum yields and lifetimes of both the systems have been found to be significantly lower than that of the parent fluorophore indicating the occurrence of photoinduced electron transfer (PET) between the terminal moieties. PET is found to be more efficient in II, presumably due to the presence of more than one electron-donating centre in the receptor moiety. Fluorescence decay behaviour of the systems suggests a through-space nature of PET. The systems exhibit off-on fluorescence signalling in the aprotic media in the presence of several metal ions, some of which are well known for their fluorescence quenching abilities. Diazacrown derivative, II, appears to be a somewhat better signalling system than the monoazacrown derivative, I.

Transition metal ions are notorious for their fluorescence quenching abilities. In this paper, we discuss the design strategies for the development of efficient off-on fluorescence signalling systems for the transition metal ions. It is shown that even simple fluorophore-spacer-receptor systems can display excellent off-on fluorescence signalling towards the quenching metal ions when the fluorophore component is chosen judiciously.

Photophysical properties of two bichromophoric systems comprising a pyridyl moiety and a naphthyl/pyrenyl moiety covalently linked through a dimethylene bridge have been investigated. The spectral behavior of the systems suggests the formation of an intramolecular complex between the two terminal moieties of the molecules in the ground state. Interestingly, no intermolecular complexation could be observed with a 1:1 mixture of the constituting components. This contrasting behavior has been interpreted taking into consideration the difference in the entropy change associated with the complexation process. Based on the effect of solvent polarity on the absorption and emission behavior of the complex and taking into consideration the molecular geometry, it is concluded that the interaction between the aromatic hydrocarbon and pyridyl moieties is primarily driven through an overlap of the π-clouds.

Three-component systems, 1a−c and 2a,b, comprising 1,8-naphthalimide and 4-methoxy-1,8-naphthalimide as fluorophore, a dimethylamino moiety as guest binding site and a polymethylene group as spacer, have been synthesized and the fluorescence behavior of these systems has been studied in the absence and in the presence of the salts of several transition metal ions. The systems are found to be very weakly fluorescent compared to their constituent fluorophores (3 and 4) and this observation has been ascribed to photoinduced intramolecular electron transfer (PIET) between the electron rich amino moiety (donor) and relatively electron deficient fluorophore component (acceptor). Spectral and electrochemical data indicate the thermodynamic feasibility of PIET (exergonic free energy changes) in these multicomponent systems and PIET is found to be most efficient in systems where the fluorophore and the amino moiety are separated by two methylene groups. Fluorescence decay behavior of the systems suggest that PIET ...

The photophysical behaviour of two carbostyrils used as layer dyes has been investigated. From a study of the solvent polarity dependence of the fluorescence properties we have shown that twisting of the amino or dimethylamino group does not affect the photophysical behaviour of carbostyrils. The results of AM1 calculations clearly show unfavourable energetics for the rotary decay process in carbostyrils. The keto form of the carbostyrils is shown to be the only absorbing and emitting species. In light of the present results, a reinvestigation of the fluorescence properties of structurally similar coumarins seems to be necessary.

Mycobacterium tuberculosis (Mtb) is the causative agent of the deadly disease tuberculosis. Iron acquisition, regulation and storage are critical for the survival of this pathogen within a host. Thus, understanding the mechanisms of iron metabolism in Mtb will shed light on its pathogenic nature, as iron is important for infection. Ferritins are a superfamily of protein nanocages that function in both iron detoxification and storage, and Mtb contains both a predicted ferritin and a bacterioferritin. Here, the cloning, expression, purification, crystallization and preliminary X-ray diffraction analysis of the ferritin homolog (Mtb BfrB, Rv3841) is reported. An Mtb BfrB crystal grown at pH 6.5 using the hanging-drop vapor-diffusion technique diffracted to 2.50 A resolution and belonged to space group C2, with unit-cell parameters a = 226.2, b = 226.8, c = 113.7 A, β = 94.7° and with 24 subunits per asymmetric unit. Furthermore, modeling the crystal structure of a homologous ferritin into a low-resolution small-angle X-­ray scattering (SAXS) electron-density envelope is consistent with the presence of 24 subunits in the BfrB protein cage quaternary structure.

Congenital patellar syndrome is bilateral isolated absence of patella. Congenital patellar aplasia or hypoplasia associated with genetic disorders belongs to a clinically diverse and genetically heterogeneous group of lower limb malformations. Absence of patella as an isolated anomaly is extremely rare and we discuss such a case in a 9-year-old boy.

An abasic site-containing DNA combined with lumiflavin allows amperometric determination of single nucleotide polymorphism through hydrogen bond-mediated nucleobase recognition in water by using abasic sites as a molecular recognition field.

In combination with abasic site (AP site)-containing DNAs, potential use of a biotic fluorescence compound, Vitamin B2 (riboflavin), is demonstrated for the fluorescence detection of the thymine (T)-related single-nucleotide polymorphisms. Our method is based on construction of the AP site in DNA duplexes, which allows small ligands to bind to target nucleotides accompanied by fluorescence signaling: an AP site-containing probe DNA is hybridized with a target DNA so as to place the AP site toward a target nucleobase, by which hydrophobic microenvironments are provided for ligands to recognize target nucleotides through stacking and hydrogen-bonding interactions. In 10 mM sodium cacodylate buffer solutions (pH 7.0) containing 100 mM NaCl and 1.0 mM EDTA, Vitamin B2 is found to selectively bind to T (K11=1.8x10(6) M(-1) at 5 degrees C) over other nucleobases, and this is accompanied by significant quenching of its fluorescence. While the sensing functions depend on the flanking sequences to the AP site, Vitamin B2 is applicable to the detection of T/C (cytosine), T/G (guanine) and T/A (adenine) mutation sequences of the CYP2A6 gene, where the flanking nucleobases are guanines in both positions (-GXG-, X=AP site).

Fluorescence of 1a and 1b is ‘switched on’ by the quenching transition metal ions and the extent of fluorescence enhancement is found to be considerably higher than that expected on the basis of photoinduced intramolecular electron transfer in the systems. The observation has been rationalised taking into account the hydrated nature of the transition metal salts and preferential solvation of the fluorophore by the water molecules.

Among the various factors determining the successful operation of an industry, one of the most crucial factors is its pricing strategy. A correct pricing strategy will help in rational allocation of scarce resources and capital formation, which is crucial for the future growth of industries. It is, however, pertinent that before one strikes at the right pricing pattern and the factors governing it, one has to be familiar with the theoretical framework of the general pricing systems so as to enable the researcher and the policy maker to examine the empirical reality of any pricing policy that is in existence. It is in this context that the present study makes an attempt at investigating the behavioural pattern of the pricing strategy of tea.

Sensing of alkali metal ions has attracted considerable interest owing to the significance of these metal ions in biology. Of the many mechanisms used for ion signaling, photoinduced electron transfer (PET) is the one most commonly exploited. We report the use of simple PET sensors as a ratiometric sensor towards alkali metal ions. The systems described here behave either as a simple PET sensor or as a ratiometric sensor towards alkali metal ions based on the length of the spacer that connects the donor and acceptor groups. The formation of an exciplex between the donor and acceptor groups in the metal ion free state and the changes of the monomer and the exciplex emissions on metal ion binding are utilized for the ratiometric signaling of alkali metal ions.

The fluorescence response of two fluorophore–spacer–receptor systems, 1 and 2, wherein a 4-aminophthalimido moiety is linked to a monoaza- and a tetraazacrown macrocycle via a dimethylene spacer, has been explored in the absence and in the presence of various transition and post transition metal ions. Unlike the parent fluorophore, these systems are weakly fluorescent because of photoinduced electron transfer (PET) between the terminal moieties of the molecules. Of the two systems, PET is found to be more efficient in 2, which contains the tetraazacrown moiety as the receptor. Both systems display complex fluorescence decay behaviour with the average fluorescence lifetime much shorter than that of the parent fluorophore. The systems exhibit fluorescence enhancement in the presence of the metal ions, some of which are notorious quenchers of fluorescence. While the fluorescence output of 1 is rather similar with different metal ions, 2 exhibits high fluorescence enhancement with metal ions such as Zn2+, Cd2+, Pb2+, Hg2+ and Mn2+ while producing negligible enhancement with the remaining metal ions studied. This specific signaling behaviour of 2 has been rationalized taking into consideration somewhat unusual binding ability of the tetraazacrown receptor moiety.

A series of 145 patients (77 males and 68 females) with fracture of the neck of the femur treated by primary replacement arthroplasty (prosthesis) is presented. The indications, complications and results of operation are discussed. Prosthetic replacement has yielded satisfactory results in 91.7 per cent of cases and is a particularly suitable procedure for Indians.

A clinico-radiological study conducted on 124 patients including 89 cases of spinal canal stenosis and 143 normal (control) individuals is presented and the various causes of stenosis of the spinal canal are reviewed. Evaluation of canal to body ratio using plain radiographs of lumbo-sacral spine based on the Jones and Thomson technique and myelography were found very useful in diagnosing spinal canal pathology preoperatively. Spinal stenosis is more common in males, predominantly in the fourth decade. Extensive decompression laminectomy in appropriately selected cases yielded satisfactory results, any associated prolapse intervertebral disc requiring excision of the herniated disc in addition to laminectomy.

The orthopaedic surgeon practising in developing countries faces multi-various problems. A large number of them are locally trained, but by experts with a strong bias towards modern methods of management of orthopaedic problems — for example, rigid internal fixation because of their earlier background training. Many of them seek and obtain from some of the best schools in Europe and the North American continent. They are all trained in the use of excellent internal fixation devices of high quality steel, vitallium or titanium. Implants of a similar composition (such as semi and total hip replacements); compatible screws and other ancillary devices; power tools (either electrically or pneumatically operated); and a clean, virtually bacteriologically sterile atmosphere with pin-point operating lights and television-monitored radiological equipment, with which he could accurately direct his guide pins so that fixation after reduction in a majority of cases is practically anatomical, form the basis of his training programme. After about five years of such training he returns to his home country, full of enthusiasm, quite frequently with equipment and implants which he is sure he can use with missionary zeal. He finds that the only place he can practice such a calibre of operative orthopaedics is a teaching hospital, either in the federal or provincial capital where there is already an entrenched, highly skilled, politically well-connected surgeon, with an established practice. He quite frequently joins the public service system and is posted as orthopaedic surgeon to a district headquarters hospital — probably the first orthopaedic surgeon ever to be posted at such an institution.

We investigated the pattern of genetic susceptibility to rheumatic diseases in Indians by means of HLA analysis. HLA B27 was present in more than 90% of cases included under the broad category or seronegative spondarthritides. In this respect our data resembled results reported for Caucasian populations. In our population, however, the phenotypic frequency of HLA B27 was low as reported from Japan.

Two new multicomponent systems with fluorophore-spacer-receptor architecture employing 4-aminophthalimide and 4-amino-1,8-naphthalimide fluorophores and aniline receptor have been developed and their fluorescence response towards quenching transition metal ions and protons has been investigated. The low fluorescence quantum yields of the supramolecular systems compared with those of the free fluorophores have been interpreted in terms of photoinduced intramolecular electron transfer (PET) in the systems. In the presence of the d-block metal ions, known for their quenching abilities, the supramolecular systems exhibit fluorescence enhancement rather than quenching. This observation has been interpreted taking into consideration of PET-quenched short fluorescence lifetime of the fluorophores. The systems reported here can be considered as potential candidates as fluorosensors for the transition metal ions and protons.

Fluorescence of 1a and 1b is ‘switched on’ by the quenching transition metal ions and the extent of fluorescence enhancement is found to be considerably higher than that expected on the basis of photoinduced intramolecular electron transfer in the systems. The observation has been rationalised taking into account the hydrated nature of the transition metal salts and preferential solvation of the fluorophore by the water molecules.